Real-time analysis for cross-linked peptides

ABSTRACT

Disclosed herein are methods for large-scale, high-throughput identification of protein-protein interactions and the topologies thereof under physiologically relevant conditions. In one aspect, the disclosure provides methods for identifying one or a plurality of interacting peptides within a biological system comprising obtaining a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker, cleaving the PIR crosslinker to produce released peptides and cleaved reporter ions, and analyzing the population of released peptides to identify interacting peptides. Also disclosed are methods for identifying candidate drug compounds, as well as methods of data processing and visualization of protein-protein interactions.

This application claims the benefit of U.S. Provisional Application No. 61/825,901, filed May 21, 2013, the disclosure of which is explicitly incorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under 5R01GM097112 and 5R01GM086688 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND

Proteins are the principal operatives within cells, involved in carrying out essentially all biological functions. A complex network of intra- and intermolecular interactions, post-translational modifications and abundance levels is required to maintain the delicate balance of function essential for life. Subtle changes within this network can give rise to specific biological responses to environmental factors, onset of disease, normal aging, and other biological processes. Therefore, direct experimental observation of protein structures and interactions in relation to biological function is paramount to improved understanding of living systems.

The versatility of protein function has its origins in topological shapes and features that these polymeric macromolecules can adopt. Moreover, the crowded intracellular environment profoundly influences their shape such that proteins that appear unstructured in vitro can adopt a more defined conformation inside cells. These induced topological features occur as a consequence of interaction within cellular compartments that may not be replicated in cell lysates or purified components.

Thus, there is a need in the art for methods that can reveal information about global protein topology under physiologically relevant conditions within native interactions and with intended partners inside cells, and a further need for methods that can do so with high sensitivity, specificity, and efficiency on a large scale.

SUMMARY

The present invention provides certain advantages and advancements over the prior art. In particular, the present disclosure provides methods for large-scale, high-throughput identification of protein-protein interactions and the topologies thereof under physiologically relevant conditions.

In one aspect, the disclosure provides methods for identifying one or a plurality of interacting peptides within a biological system, comprising: (a) obtaining a population of cross-linked precursor peptides produced by digestion of a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker; (b) subjecting the population of cross-linked precursor peptides to mass spectrometry (MS) to produce precursor ions; (c) subjecting precursor ions with a charge state equal to or greater than a cutoff charge state to conditions under which the cleavable PIR cross-linker is cleaved, thereby producing a population of released peptides and cleaved reporter ions; and (d) analyzing the population of released peptides to identify interacting peptides, wherein identifying interacting peptides comprises identifying released peptides that, when added to the mass of the reporter ion, have a combined mass equal to the mass of the corresponding precursor ion.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating cancer comprising: (a) contacting a peptide pair from the group consisting of:

(i) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 1) FYEQFSKNIK; (ii) (SEQ ID NO: 2) FYEAFSKNLK, (SEQ ID NO: 2) FYEAFSKNLK; (iii) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 2) FYEAFSKNLK; (iv) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 3) KHLEINPDHPIVETLR; (v) (SEQ ID NO: 4) APFDLFENKK, (SEQ ID NO: 1) FYEQFSKNIK; (vi) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 5) KAAALEAMK; and (vii) (SEQ ID NO: 2) FYEAFSKNLK, (SEQ ID NO: 5) KAAALEAMK; with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating cancer.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating an antibiotic-resistant infection comprising: (a) contacting a peptide pair comprising KINLYGNALSR (SEQ ID NO: 6) and NDIAPYLGFGFAPKINK (SEQ ID NO: 7) with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating an antibiotic-resistant infection.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating A. baumannii infection comprising: (a) contacting a peptide pair from the group consisting of:

(i) (SEQ ID NO: 8) VFFDTNKSNIKDQYKPEIAK, (SEQ ID NO: 9) MSAAEAVKEK; (ii) (SEQ ID NO: 10) TKEGR, (SEQ ID NO: 9) MSAAEAVKEK; and (iii) (SEQ ID NO: 11) LSTQGFAWDQPIADNKTK, (SEQ ID NO: 9) MSAAEAVKEK; with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating A. baumannii infection.

In another aspect, the disclosure provides cleavable protein interaction reporter (PIR) cross-linkers comprising formula (I):

(SEQ ID NO: 27) wherein X is H, succinimid-N-yl, or phthalimid-N-yl; and Y is H or a capture moiety.

In another aspect, a method is provided. A computing device receives data representing a first protein structure. The computing device receives data representing a second protein structure. The computing device receives data representing an interaction between the first protein structure and the second protein structure. The computing device generates a display. The display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.

In another aspect, a computing device is provided. The computing device includes a processor and a tangible computer-readable medium. The tangible computer-readable medium is configured to include comprise instructions that, when executed by the processor, are configured to cause the computing device to perform functions. The functions include: receiving data representing a first protein structure; receiving data representing a second protein structure; receiving data representing an interaction between the first protein structure and the second protein structure; and generating a display, where the display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.

In another aspect, a tangible computer-readable medium is provided. The tangible computer-readable medium is configured to include comprise instructions that, when executed by a processor of a computing device, are configured to cause the computing device to perform functions. The functions include: receiving data representing a first protein structure; receiving data representing a second protein structure; receiving data representing an interaction between the first protein structure and the second protein structure; and generating a display, where the display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.

In another aspect, a device is provided. The device includes: means for processing; means for receiving data representing a first protein structure; means for receiving data representing a second protein structure; means for receiving data representing an interaction between the first protein structure and the second protein structure; and means for generating a display using the processing means, where the display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.

These and other features and advantages of the present invention will be more fully understood from the following detailed description of the invention taken together with the accompanying claims. It is noted that the scope of the claims is defined by the recitations therein and not by the specific discussion of features and advantages set forth in the present description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description of the embodiments of the present invention can be best understood when read in conjunction with the following drawings, in which:

FIG. 1 shows, at left, a flow chart depicting an LC-MS algorithm functions during LC-MS experiments. At right is an idealized practical diagram of how the algorithm would operate on real data directly corresponding to the flow chart.

FIGS. 2A-2C. Protein interaction reporter (PIR) molecules which have been used in this study. FIG. 2A: Biotin Aspartate Proline N-Hydroxyphlalamide (BDP-NHP). FIG. 2B: Biotin Rink N-Hydroxysuccinimide (BRink-NHS). FIG. 2C: Rink N-Hydroxysuccinimide (2Rink-NHS).

FIG. 3. REACT algorithm permits targeting released peptide products from cross-linked pairs to increase peptide identification probability. FIG. 3 presents example MS, MS², and MS³ spectra of a cross-linked homodimer peptide pair (K.GNGKSSDPAGSFR.V (SEQ ID NO: 12)) to demonstrate this capability.

FIGS. 4A-4C. FIG. 4A: High resolution MS² spectra acquired on a cross-linked species with two different cross-linkers within the same LC-ReACT experiment. The cross-linked site identified involves the same two peptides from RNase A (ETAAAKFER (SEQ ID NO: 13) and NLTKDR (SEQ ID NO: 14)). The top contains this site identified with BDP cross-linker, and the bottom contains this site identified with 2Rink cross-linker. Low resolution MS³ used to make peptide sequence identification for NLTKDR (SEQ ID NO: 14) (FIG. 4B) and ETAAAKFER (SEQ ID NO: 13) (FIG. 4C) for both linkers.

FIGS. 5A-5E show an example of ReACT data acquired from PIR-labeled E. coli cells. FIG. 5A: High resolution MS¹ acquisition for precursor information; inset is an expanded view of the spectrum surrounding the cross-linked peptide precursor, 718.174 m/z. FIG. 5B High resolution MS² acquisition for cross-linked peptide relationship information. FIGS. 5C-5D: Low resolution MS³ acquisition for peptide sequence information (HFTAKLK (SEQ ID NO: 15); GLTFTYEPKVLR (SEQ ID NO: 16)). FIG. 5E: Tryptophanase crystal structure (E. coli, PDB: 2OQX) with all observed cross-links marked in grey; the cross-link observed in this data is marked in red, while other sites we observe in additional relationships are in grey.

FIGS. 6A-6F. Cellular cross-linking results obtained with ReACT from both E. coli and HeLa experiments. FIG. 6A: A breakdown of the type of cross-links observed from E. coli (inter-protein, intra-protein, or unambiguous homodimer). FIG. 6B: Protein localization of proteins identified in cross-linked peptide pairs from E. coli. FIG. 6C: Protein interaction network constructed from all cross-links observed within E. coli cell experiments. FIGS. 6D-6F: Same information for HeLa cells.

FIG. 7. E. coli 30 s ribosome (PDB: 3FIH) with 3 of 4 observed heterodimeric ribosomal cross-links mapped (RNA has been omitted).

FIG. 8. Distribution of mass errors for 648 PIR relationships. Mass error is calculated as 10⁶*|(mass cross-linked precursor−(mass peptide 1+mass peptide 2+mass reporter))|/mass cross-linked precursor.

FIG. 9A: Protein interaction network generated exclusively from cross-linking results. Network consists of 307 nodes representing proteins connected by 446 edges representing observed intraprotein and interprotein cross-links. Nodes are shaded according to subcellular localization with major hubs indicated by larger node size. Bold black edges indicate cross-links for which both peptides were identified at less than 5% FDR whereas thin dashed edges are cross-links for which only one peptide passed the FDR threshold. FIG. 9B: Distribution of nodal distance generated using xlink:DB to compare protein interactions from network in A with protein-protein interactions in the IntAct database. FIG. 9C: Pie chart indicating cross-links that can be mapped to existing structures in the PDB and those providing new topological information. FIG. 9D: Pie chart indicating subcellular localization of cross-linked proteins.

FIGS. 10A-10C. Confocal microscopy images of PIR labeled HeLa cells. FIG. 10A: neutravidin green staining; FIG. 10B: propidium iodide staining; FIG. 10C: negative control.

FIG. 11A: Precursor FT-ICR mass spectrum for with inset illustrating the 4+ isotope distribution at m/z 910.198 for the homodimer cross-linked peptide pair. FIG. 11B: High resolution MS² spectrum for cross-linked peptide pair indicating released peptide and reporter ions. FIG. 11C: Ion trap MS³ spectrum used to identify peptide FYEAFSKNLK (SEQ ID NO: 2) from HS90B. FIG. 11D: Crystal structure for the yeast HSP90 dimer (PBD: 2CG9) highlighting position of cross-linked lysine 434 from HS90B near the interface of the middle and C-terminal domains (note: particular lysine residue is conserved between yeast and human although appears as K423 in yeast crystal structure). FIG. 11E: Predicted disorder plot (generated using VSL2 disorder prediction algorithm) for HS90B indicating presence of K434 near a transition between order and disordered region.

FIG. 12A-12D. Mass spectra identifying the hetero-dimer cross-link between heat shock protein 90-alpha and heat shock protein 90-beta (peptides FYEAFSKNLK (SEQ ID NO: 2); FYEQFSKNIK (SEQ ID NO: 1).

FIG. 13. Crystal structure of glutamate dehydrogenase (PDB: 1L1F) illustrating cross-linked site at lysine 480 at the tip of the antenna domain. (Note that K480 is labeled as K479 in the figure due to absence of N-terminal Met residue from the start codon in the crystal structure.)

FIGS. 14A-14C. Cross-links mapped onto structure of nucleosome (PDB: 3AFA). FIG. 14A: Individual monomer structures of the four core histone proteins with cross-linker reactive lysine residues highlighted in space filling display. N-terminal and C-terminal tails not present in the crystal structure were drawn in manually (indicated by dashed lines) to illustrate cross-linked sites in these highly disordered regions. FIG. 14B: Tetramer structures for H32-H42 and H2A2-H2B2 with intraprotein and interprotein cross-links displayed as dashed lines. FIG. 14C: Complete nucleosome particle including 137 bp DNA wrapped around histone octamer complex with cross-links displayed.

FIG. 15. Cross-link map of histone H3 including post-translational modifications. Sequence of histone H3 from residues 0-79 (SEQ ID NO: 17) with cross-linked sites highlighted in bold with residue numbers in superscript. Mapped cross-links are shown below and include post-translational modifications as indicated in the key. Venn diagram illustrates overlap of cross-links observed between unmodified, acetylated, or methylated (mono-, di-, tri-methylation grouped together). Extracted ion chromatographs are included for cross-linked peptides (KSTGGKAPR (SEQ ID NO: 18); KQLATK (SEQ ID NO: 19)) linking K14-K18 illustrating chromatographic resolution of various modified forms of this cross-linked peptide pair.

FIG. 16. Model structures for PHB-PHB homodimer and PHB-PHB2 dimer generated through homology modeling and molecular docking using distance constraints from cross-linked residues. The cross-linked sites PHB K201 and PHB2 K215 are located in the C-terminal domain thought to be important for stabilizing this interaction.

FIGS. 17A-17D. Comparison of models for PHB-PHB homodimer, and PHB-PHB2 heterodimer for which cross-linking distance constraints were applied (FIGS. 17A and 17B) and were not applied (FIGS. 17C and 17D).

FIGS. 18A-18B. FIG. 18A: Protein kinase a holoenzyme structure (R2C2) assembled from known crystallographic and cross-linking data. Cross-links obtained using REACT are shown through denoting the lysine in the primary sequence which was found labeled and shown in space-filling form. The section between the two crystallized regions is displayed as a dotted line, because no spatial experimental data is available. However, cross-linking data obtained supports close proximity of the disorder linker region between the N-terminal and C-terminal regions with existing crystallographic data. FIG. 18B: RIα dimer upon binding with cAMP and release of the catalytic subunits.

FIG. 19. SDS-PAGE separation of in vitro PKA experiments. Lanes are labeled accordingly along the top of the gel. Boxes indicate sections excised for in-gel digest ReACT analysis.

FIGS. 20A-20B. Histogram of relationship mass error determined by ReACT for both E. coli (FIG. 20A) and HeLa cell experiments (FIG. 20B).

FIG. 21A depicts a web structure for the XLink-DB system, in accordance with an example embodiment. XLink-DB allows loading, visualization and analysis of protein-protein interaction data acquired with chemical cross-linking and mass spectrometry. Cross-linked peptides are mapped against protein structured downloaded from PDB so that cross-linked sites can be automatically visualized on protein structures. A Cytoscape interaction network is created with XLink-DB so that all identified protein-protein interactions can be visualized. This network is mapped against existing protein-protein interaction databases acquired with yeast two hybrid, co-IP other technologies.

FIG. 21B is a flowchart for a data process algorithm for the XLink-DB system, in accordance with an example embodiment.

FIG. 21C is a flowchart for an algorithm for choosing PDB structures by the XLink-DB system, in accordance with an example embodiment.

FIG. 22 depicts a distribution of interlinked distances of large-scale cross-linked peptide data sets from cells and cell lysates, in accordance with an example embodiment.

FIG. 23 depicts a distribution of the node distances observed in cross-linked peptide data sets from cell lysates and intact cells as determined from the E. coli protein interaction database EciD, in accordance with an example embodiment.

FIG. 24A is a block diagram of an example computing network, in accordance with an embodiment.

FIG. 24B is a block diagram of an example computing device, in accordance with an embodiment.

FIG. 25 is a flowchart for an example method for generating a display of multiple protein structures, in accordance with an example embodiment.

Skilled artisans will appreciate that elements in the figures are illustrated for simplicity and clarity and have not necessarily been drawn to scale. For example, the dimensions of some of the elements in the figures can be exaggerated relative to other elements to help improve understanding of the embodiment(s) of the present invention.

DETAILED DESCRIPTION

All publications, patents, and patent applications cited herein are hereby expressly incorporated by reference for all purposes.

Before describing the present invention in detail, a number of terms will be defined. As used herein, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. For example, reference to a “protein” means one or more proteins.

It is noted that terms like “preferably”, “commonly”, and “typically” are not used herein to limit the scope of the claimed invention or to imply that certain features are critical, essential, or even important to the structure or function of the claimed invention. Rather, these terms are merely intended to highlight alternative or additional features that can or cannot be used in a particular embodiment of the present invention.

For the purposes of describing and defining the present invention it is noted that the term “substantially” is used herein to represent the inherent degree of uncertainty that can be attributed to any quantitative comparison, value, measurement, or other representation. The term “substantially” is also used herein to represent the degree by which a quantitative representation can vary from a stated reference without resulting in a change in the basic function of the subject matter at issue.

All embodiments of the invention can be used in combination with any other embodiment(s) of any aspect of the invention unless the context clearly indicates otherwise.

In one aspect, the disclosure provides methods for identifying one or a plurality of interacting peptides within a biological system, comprising: (a) obtaining a population of cross-linked precursor peptides produced by digestion of a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker; (b) subjecting the population of cross-linked precursor peptides to mass spectrometry (MS) to produce precursor ions; (c) subjecting precursor ions with a charge state equal to or greater than a cutoff charge state to conditions under which the cleavable PIR cross-linker is cleaved, thereby producing a population of released peptides and cleaved reporter ions; and (d) analyzing the population of released peptides to identify interacting peptides, wherein identifying interacting peptides comprises identifying released peptides that, when added to the mass of the reporter ion, have a combined mass equal to the mass of the corresponding precursor ion.

The methods of the invention are useful, for example, to identify cross-linked peptide pairs using mass spectrometry cleavable cross-linkers that are directly integrated into the mass spectral acquisition. These methods, provide significant improvement over current detection and identification limits of cross-linked peptide pairs by focusing the analysis time and instrument duty cycle on those ions which specifically meet the mass relationships engineered in PIR chemical cross-linkers or similar molecules. Operational time is reduced by not having to perform post-acquisition data analysis beyond that of a proteome database search. The methods of the invention are compatible for use with any mass spectrometry cleavable cross-linker. The methods of the invention facilitate studies using a wide range of cross-linker chemistries for PPI and topology interrogation within complex biological systems, and as shown, even in human cells. The methods of the invention enable large-scale identification of cross-linked species from cells, on the order of 1000 s of cross-linked species, which represents a 10- to 100-fold improvement over any previous method. With these methods, proteome-wide PPI identification and topological analyses are possible.

As used herein, the term “protein interaction reporter” (“PIR”) refers to any cleavable cross-linker that can yield expected mass relationships between a cross-linked precursor and the peptides released after cleavage of the PIR.

As used herein, the terms “polypeptide,” “protein,” and “peptide” all refer to a chain, usually unbranched, of amino acid monomers linked by peptide bonds. Typically, “peptide” refers to a protein fragment or small protein of less than about 100 amino acids in length. As used herein, the terms “residue” and “protein residue” are interchangeable and refer to an amino acid that is bonded with other amino acids by one or more peptide bonds within a protein.

As used herein, the term “MS^(n)” refers to a mass spectrometry (MS) analysis of order n. Thus, MS¹ refers to a first mass spectrometric analysis (e.g. the first quadrupole) in a multi-stage mass spectrometer; MS² refers to a second stage of mass spectrometric analysis; and MS³ refers to a third stage of mass spectrometric analysis. As used herein, the terms “MS/MS” and “tandem mass spectrometry” are interchangeable and refer to mass spectrometric analysis with two stages. As used herein, the term “MS/MS/MS” refers to mass spectrometric analysis with three stages. For any stage of mass spectrometry, any suitable type of ion source can be used with the methods and compositions disclosed herein, including but not limited to electrospray ionization (ESI), electron impact ionization (EI), fast atom bombardment (FAB), chemical ionization (CI), atmospheric pressure chemical ionization (AFCI), and matrix-assisted laser desorption/ionization (MALDI). For any stage of mass spectrometry, any suitable type of mass analyzer can be used with the methods and compositions disclosed herein, including but not limited to time-of-flight (TOF) analyzers, quadrupole mass analyzers, ion traps, quadrupole ion traps (three-dimensional, linear, or toroidal), cylindrical ion traps, orbitraps, and Fourier transform ion cyclotron resonance analyzers.

As used herein, the term “protein-protein interaction” (“PPI”) refers to physical contacts established between two or more proteins as a result of biochemical events and/or electrostatic forces.

As used herein, the term “topology” or “topological” refers to the geometric and spatial information regarding the interaction between two proteins. In the case where two proteins interact, topological information can include the amino acid residues of each protein that interact, the orientation of the interacting proteins with respect to one another, the orientation of the interacting amino acid residues with respect to one another or with respect to the proteins, three-dimensional structures of the protein surfaces that interact, the sites on the overall three dimensional protein structures governing the interaction, etc.

As used herein, the term “digest” or “digestion” refers to any means, such as proteolysis or proteolytic digestion, of splitting or degrading a protein into smaller peptide fragments. Many enzymes are capable of digesting proteins. These proteolytic enzymes (proteases) are commonly divided into six broad groups: serine proteases, threonine proteases, cysteine proteases, aspartate proteases, glutamic acid proteases, and metalloproteases. Examples of proteases commonly used in conjunction with mass spectrometry include trypsin (which cleaves the carboxyl side of arginine and lysine residues), LysN (which cleaves the amino side of lysine residues), LysC (which cleaves the carboxyl side of lysine residues), GluC (which cleaves the carboxyl side of glutamate), AspN (which cleaves the amino side of aspartate residues), and chymotrypsin (which cleaves the carboxyl side of tyrosine, phenylalanine, tryptophan and leucine).

As used herein, the term “cross-link” refers to a bond, usually a covalent bond, that links one biopolymer chain, such as a protein chain, to another. As used herein, the terms “cross-linking reagent,” “cross-linking agent,” or “cross-linker” are interchangeable and refer to a reagent or set of reagents capable of chemically linking two molecules, for example two proteins, by one or more bonds, for example covalent bonds.

In general, chemical cross-linkers compatible with the methods disclosed herein possess a cleavage site, such as a low-energy CID cleavage site, to facilitate cross-linked peptide relationship recognition and subsequent MS³ peptide fragmentation pattern acquisition. Non-limiting examples of PIR cross-linkers suitable for use with the disclosed methods are shown in FIG. 2. Although these compounds have a variety of structural and chemical properties, each contains the basic features of a mass-coded reporter ion and two low-energy CID cleavable bonds. In addition, the biotin-aspartate-proline (BDP) and BRink cross-linkers include a biotin moiety, useful for affinity purification of the conjugated reaction products. Among the benefits of using PIR cross-linkers are the engineered fragmentation patterns and the use of a reporter ion as an indicator of labeled species.

As used herein, the term “precursor” refers to a cross-linked molecule prior to the cleavage of the crosslink. Thus, in the case where a PIR cross-links two peptides, the precursor comprises the PIR cross-linker that is covalently attached to both peptides. Cleavage of the precursor yields at least one peptide and a reporter moiety.

In some embodiments of the methods disclosed herein, the population of cross-linked precursor peptides are obtained by contacting a biological system with a cleavable protein interaction reporter (PIR) cross-linker to produce cross-linked proteins, and obtaining the cross-linked precursor peptides therefrom.

In some embodiments, the methods further comprise purifying and digesting the cross-linked proteins to obtain the cross-linked precursor peptides. Purification of cross-linked peptides is used to allow those species to be detected with improved signal-to-noise ratio in the mass spectrometer. Purification is particularly beneficial with samples derived from cells, since the relative abundance of cross-linked peptides from in vivo cross-linking compared to non-cross-linked peptides is low. However, the disclosed methods can function to identify cross-linked peptides irrespective of purification, as long as the target ions are detectable in the samples. For solutions of pre-purified proteins that are cross-linked, for example, no affinity purification is needed and the disclosed methods operate to allow identification of cross-linked peptides.

In some embodiments, the biological system comprises a cell, tissue, cell lysate, blood, serum, sputum, or urine. As used herein, the term “biological system” refers to any set of molecules, cells, organisms, solutions, reagents, tissues, or other materials, which has any biological relevance. Examples of biological systems within the meaning of the disclosure include cells, cell lysates, cell cultures, tissues, organs, organisms, growth media, culture media, biological secretions, serum, blood, urine, feces, solutions or suspensions comprising proteins or peptides, etc.

In some embodiments of the disclosed methods, the conditions under which the cleavable PIR cross-linker is cleaved comprise collision-induced dissociation (CID). In mass spectrometry, “collision-induced dissociation” (“CID”), also known as “collisionally activated dissociation” (“CAD”), is a mechanism by which to fragment molecular ions in the gas phase. The molecular ions are usually accelerated by some electrical potential to high kinetic energy and then allowed to collide with neutral molecules (often helium, nitrogen or argon). In the collision some of the kinetic energy is converted into internal energy which results in bond breakage and the fragmentation of the molecular ion into smaller fragments. These fragment ions can then be analyzed by a mass spectrometer. For example, in a triple quadrupole mass spectrometer there are three quadrupoles. In one mode of operation, the first quadrupole (“Q1”) can act as a mass filter and transmits a selected ion and accelerates it towards “Q2,” a collision cell. The pressure in Q2 is higher and the ions collides with neutral gas in the collision cell and fragments by CID. The fragments are then accelerated out of the collision cell and enter “Q3” which scans through the mass range, analyzing the resulting fragments (as they hit a detector). This produces a mass spectrum of the CID fragments from which structural information or identity can be gained. Many other experiments using CID on a triple quadrupole exist, such as the methods disclosed herein.

In some embodiments, the population of released peptides in step (d) is analyzed using MS². In some embodiments the step (d) analysis comprises the isolation, fragmentation, and analysis of one precursor molecule at a time. In other embodiments, the step (d) analysis comprises multiplexed testing, wherein more than one precursor is isolated, fragmented and analyzed at a time. In such an embodiment, several 4+ or higher ions are isolated and fragmented simultaneously so that the disclosed methods are used to simultaneously find and identify released peptides from more than one cross-linked precursor.

In some embodiments, identifying interacting peptides in step (d) further comprises first identifying released peptides with masses lower than partial cleavage products prior to identifying released peptides that, when added to the mass of the reporter ion, have a combined mass equal to the mass of the corresponding precursor ion. In some embodiments, identifying released peptides with masses lower than partial cleavage products comprises identifying released peptides with masses that are less than the mass of the corresponding precursor ion minus the mass of the reporter ion minus the mass of lysine stumps, wherein lysine stumps are residual modifications that remain on lysine residues after cleavage.

In some embodiments, the methods disclosed herein further comprise determining the identities of the interacting peptides by subjecting the interacting peptides to conditions that cause peptide fragmentation to yield spectra that can be identified from genomic, proteomic, or other large protein sequence databases. In some embodiments, the identities of the interacting peptides are determined by MS³.

In some embodiments, the MS³ step takes place immediately after the MS² step. For example, in some embodiments, the identification of released peptides is accomplished during a single liquid chromatographic (LC) separation of thousands of molecules. Each species elutes from the LC column with a retention time characteristic of its overall hydrophobic character and detectable signals for each cross-linked precursor may only persist for 15 to 30 seconds. Thus, MS³ proceeds before the detectable signals dissipate. In such a case, it is beneficial for MS³ to proceed soon after the MS² stage (during which released peptides and precursor ions are analyzed to determine if they satisfy equation (1)) because the peptides identified in MS³ are known to belong to the precursor that was analyzed by MS² moments before.

In other embodiments, MS³ does not proceed immediately after MS². Rather, MS³ may be performed at a later time and/or a separate location. In such a case, the ion yielding the released peptides identified in the later MS³ step must be determined to be the same ion that yielded a given retention time and precursor mass in the earlier LC-MS² analysis.

In some embodiments of the methods disclosed herein, the cutoff charge state is from 0 to +10. In some embodiments, the cutoff charge state is at least +3. In some embodiments, the cutoff charge state is at least +4. In some embodiments, the cutoff charge state is at least +5.

In some embodiments, the precursor molecule comprises two cross-linked peptides. In other embodiments, the precursor molecule comprises three cross-linked peptides and the PIR cross-linker is capable of cross-linking three proteins. In other embodiments, the precursor molecule comprises four or more cross-linked peptides and the PIR cross-linker is capable of cross-linking four or more proteins.

In some embodiments of the methods disclosed herein, the cleavable PIR cross-linker comprises formula (I):

(SEQ ID NO: 27) wherein X is H, succinimid-N-yl, or phthalimid-N-yl; and Y is H or a capture moiety. In some embodiments, the capture moiety is biotin, a hemagglutinin (HA) tag, or a polyhistidine tag.

In some embodiments of the methods disclosed herein, the cleavage condition is collision-induced dissociation (CID).

As used herein, the term “capture moiety” refers to a chemical moiety attached to a molecule that can be used to capture the molecule, for example, through interaction with another chemical moiety, for purposes such as affinity purification. For example, a biotin capture moiety can be used in conjunction with a streptavidin column to affinity purify the molecule comprising the biotin moiety. A poly-histidine tag (His-tag, 6×His-tag, hexa histidine-tag, or His6-tag) is a capture moiety comprising at least six histidine amino acid residues that can be used to capture a His-tagged molecule because the string of histidine residues binds to several types of immobilized metal ions, including nickel, cobalt and copper, under specific buffer conditions. In addition, anti-His-tag antibodies are commercially available for use in methods involving His-tagged proteins. Any protein for which an antibody specific for that protein exists can comprise a capture moiety. Other examples of capture moieties include hemagglutinin (HA) tag, streptavidin-binding peptide, calmodulin-binding peptide, S-peptide, and chitin-binding domain.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating cancer comprising: (a) contacting a peptide pair from the group consisting of:

(i) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 1) FYEQFSKNIK; (ii) (SEQ ID NO: 2) FYEAFSKNLK, (SEQ ID NO: 2) FYEAFSKNLK; (iii) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 2) FYEAFSKNLK; (iv) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 3) KHLEINPDHPIVETLR; (v) (SEQ ID NO: 4) APFDLFENKK, (SEQ ID NO: 1) FYEQFSKNIK; (vi) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 5) KAAALEAMK; and (vii) (SEQ ID NO: 2) FYEAFSKNLK, (SEQ ID NO: 5) KAAALEAMK; with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating cancer.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating cancer comprising: (a) contacting a protein pair or fragments thereof from the group consisting of:

-   -   (i) HS90A (GenBank: CAI64495.1; SEQ ID NO: 20), HS90A (GenBank:         CAI64495.1; SEQ ID NO: 20);     -   (ii) HS90B (GenBank: AAH68474.1; SEQ ID NO: 21), HS90B (GenBank:         AAH68474.1; SEQ ID NO: 21);     -   (iii) HS90A (GenBank: CAI64495.1; SEQ ID NO: 20), HS90B         (GenBank: AAH68474.1; SEQ ID NO: 21);     -   (iv) HS90A (GenBank: CAI64495.1; SEQ ID NO: 20), STIP1 (GenBank:         AAH39299.1; SEQ ID NO: 22);     -   (v) HS90B (GenBank: AAH68474.1; SEQ ID NO: 21), STIP1 (GenBank:         AAH39299.1; SEQ ID NO: 22);         with a plurality of test compounds under conditions suitable for         binding of one member of the protein pair or a fragment thereof         to the other member of the protein pair or a fragment thereof;         and (b) identifying a test compound that reduces binding of one         member of the protein pair or a fragment thereof to the other         member of the protein pair or a fragment thereof relative to a         control, wherein the identified test compound is a candidate         compound for treating cancer, and wherein pairs (i) and (ii)         represent the interaction of a protein with itself.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating an antibiotic-resistant infection comprising: (a) contacting a peptide pair comprising KINLYGNALSR (SEQ ID NO: 6) and NDIAPYLGFGFAPKINK (SEQ ID NO: 7) with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating an antibiotic-resistant infection.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating an antibiotic-resistant infection comprising: (a) contacting a protein pair or fragments thereof comprising Oxa-23 (GenBank: ACJ39972.1; SEQ ID NO: 23) and CarO (GenBank: ACN32317.1; SEQ ID NO: 24) with a plurality of test compounds under conditions suitable for binding of one member of the protein pair or a fragment thereof to the other member of the protein pair or a fragment thereof; and (b) identifying a test compound that reduces binding of one member of the protein pair or a fragment thereof to the other member of the protein pair or a fragment thereof relative to a control, wherein the identified test compound is a candidate compound for treating an antibiotic-resistant infection.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating A. baumannii infection comprising: (a) contacting a peptide pair from the group consisting of:

(i) (SEQ ID NO: 8) VFFDTNKSNIKDQYKPEIAK, (SEQ ID NO: 9) MSAAEAVKEK; (ii) (SEQ ID NO: 10) TKEGR, (SEQ ID NO: 9) MSAAEAVKEK; and (iii) (SEQ ID NO: 11) LSTQGFAWDQPIADNKTK, (SEQ ID NO: 9) MSAAEAVKEK; with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating A. baumannii infection.

In another aspect, the disclosure provides methods of identifying a candidate compound for treating A. baumannii infection comprising: (a) contacting a protein pair or fragments thereof comprising OmpA (GenBank: AAR83911.1; SEQ ID NO: 25) and desmoplakin (GenBank: AAA85135.1; SEQ ID NO: 26) with a plurality of test compounds under conditions suitable for binding of one member of the protein pair or a fragment thereof to the other member of the protein pair or a fragment thereof; and (b) identifying a test compound that reduces binding of one member of the protein pair or a fragment thereof to the other member of the protein pair or a fragment thereof relative to a control, wherein the identified test compound is a candidate compound for treating A. baumannii infection.

In another aspect, the disclosure provides cleavable protein interaction reporter (PIR) cross-linkers comprising formula (I):

(SEQ ID NO: 27) wherein X is H, succinimid-N-yl, or phthalimid-N-yl; and Y is H or a capture moiety. In some embodiments, the amino acids are L-amino acids. In some embodiments, the capture moiety is biotin, a His tag, or an HA tag.

The methods and compositions disclosed herein relate to cross-linking mass spectrometry (XL-MS). These methods involve “fixing” the biological system through covalent chemical modification of amino acid residues and investigating the cross-linked sites using mass spectrometry methods. XL-MS enables the identification of PPIs as well as unique topological features and yields large-scale data. An advantage of cross-linking is the potential to study protein topologies that cannot be readily investigated using other techniques, such as disordered protein domains and membrane proteins. Unlike X-ray crystallography or NMR structure determination, cross-linking data can provide unique structural insight on many proteins as they exist in their natural cellular environment in a single experiment. XL-MS thus has the capacity to produce large-scale data sets, although in the past, technical limitations have constrained the scope of XL-MS methods to the identification of less than 100 cross-linked peptides in vivo.

As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. The XLink-DB system, or XLink-DB for short, can include a software package that serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. Cross-linked sites are automatically mapped onto PDB structures if available, and results are compared to existing protein interaction databases. A protein interaction network is also automatically generated for the entire data set. A server with the XLink-DB system, including examples, and a help page are available for noncommercial use (see brucelab.gs.washington.edu/cross-linkdbvl/). The source code can be viewed and downloaded; e.g., see sourceforge.net/projects/cross-linkdb/?source=directory.

Protein interactions support most biological functions and are directed by the shapes or topologies of the interacting proteins. Improved measurements of protein interaction topologies in cells are needed to increase our understanding of how protein interactions carry out their life supporting functions. Chemical cross-linking with mass spectrometry has been used to study protein structures and complex topologies for several years

Most prior applications have been limited to either purified proteins or complexes due to the complexity and wide dynamic range presented by complex biological samples. Recent technical advancements of the chemical cross-linking methods achieved in a number of laboratories have allowed this technique to be extended to complex systems. Successful applications of chemical cross-linking to studies of intact virus particles, cell lysates, and even intact bacterial and human cells suggest that in the future, cross-linking methods may provide a majority of structural and topological data on protein complexes as they exist in cells or other complex samples.

As is the case with most large-scale biological data, its usage among investigators in biochemistry, biophysics, cellular and molecular biology, as well as proteomics requires that new tools be developed to visualize, share and compare these results. This is especially true for large-scale cross-linking data since current growth in data quantity exceeds manual data analysis capabilities. Furthermore cross-linking with mass spectrometry data sets are unique in that they contain multiple tiers of information on protein sequence, interaction, and structural levels for which no single existing data analysis tool can sufficiently support. Often data analysis requires comparison of cross-linking results with existing crystal structure data if available. In addition, cross-linking data are often compared with existing protein interaction data. If previously unknown interactions are discovered, the cross-linked site information can be superimposed by computational docking of interacting structures. These steps can require hours of efforts even with only a few cross-linked peptide pairs in a single experiment and this approach becomes intractable for hundreds of cross-linked peptides.

XLink-DB includes software designed to serve both as a storage site and an online data processing and visualization tool to enable analysis of large-scale cross-linked peptide data sets. Importantly, XLink-DB is useful among biological and proteomics research communities since it provides new analysis capabilities and improved access to complex cross-linking topological data.

XLink-DB allows users to upload their cross-linking data and populate a relational database, as well as browse existing data sets. As indicated in FIG. 21B, XLink-DB can use a data process algorithm for uploaded data that automatically retrieves related protein sequence information from the UniProt catalog and high resolution structure information from the Protein Data Bank (PDB). If relevant structures are available, cross-linked site annotation can be automatically performed with XLink-DB and visualized within the Jmol applet (see jmol.sourceforge.net). The cross-linking data is also visualized in a protein interaction network view with an embedded web-based Cytoscape tool. The data stored in XLink-DB can be compared to existing protein interaction databases such as IntAct and EciD. We anticipate that XLink-DB can be a useful tool and benefit the proteomics research community as well as all researchers interested in protein topologies and interactions.

Several protein interaction databases have been established and embraced by the scientific community, such as PDB, EciD and IntAct. But none of them provide protein interaction topological data that can be provided by XLink-DB. XLink-DB was developed to maximize the access and utility of protein interaction topological data that is now available and can come from these technological advancements.

XLink-DB presents a new way to organize and demonstrate protein interaction data with topological information. Conventional databases either lack the interaction information or lack the topological information for the protein complexes. With the advancement of new cross-linking technologies, large scale protein interaction studies are now becoming reality. XLink-DB is the first database to allow compilation and analysis of large-scale cross-linking data. XLink-DB can help the cross-linking community to store, share and process their data, as well as enable sharing the data with other scientists with interests in protein interactions and topologies.

The XLink-DB System

The XLink-DB system can be embodied using a computing device operating a web site. An as example of the XLink-DB system, an example XLink-DB web site can utilize PHP 5.5 and JavaScript, example XLink-DB data analysis tools can be programmed with Java 1.6, and example XLink-DB data can be stored in a relational database, such as a MySQL database. Other embodiments can utilize other software techniques and/or programming languages for the XLink-DB web site. In some embodiments, functionality of the XLink-DB web site can depend on both Java applets and flash plug-in. As shown in FIG. 21A, the XLink-DB web site contains two major modules: (1) data upload, process and storage and (2) data visualization.

Five different views (interaction network, protein structure, search, site and table views) are available for cross-linked peptide data analysis. Interaction network view shows the protein interaction network generated from the data set. Protein structure view shows the cross-linking peptide pairs on the existing PDB structure. A key feature of XLink-DB is the ability to map cross-linked sites on protein complexes for which individual protein crystal structures exist, but no cocrystals have been reported. Site view is designed to display the sites when the co crystal structure does not exist. Search view is a subnetwork of the data set. The table view is a summary of the data set in a table. To help users get familiar with the features of the database, we have created a video tutorial which can be found in the help page. In addition, we have also put tooltips on some parameters to guide the users. Details on each module are discussed below.

Data Upload, Process, and Storage

The users can choose if they want their data to be publically available. If they choose not to release their data to the public, they can get a table name after the data upload is finished and their data cannot appear in the drop-down list to choose. Instead, the users can use the table name to access their nonpublic data. Their data can be stored in the database for 90 days. If the user chooses to make their data public available, the data can be permanently stored in the database and can appear in a dropdown list in the selection box under “Choose a data set”. The users can access their published and previously uploaded data from the drop-down list. Data are uploaded in XLink-DB in a tab-delimited file format with column arrangements as indicated on XLink-DB help page (see brucelab.gs.washington.edu/cross-linkdbvl/help.php).

FIG. 21B illustrates an example data process algorithm. In this data process algorithm, XLink-DB can parse the input file to extract the UniProt identifiers for each cross-linked protein contained within the data set. The UniProt files containing protein annotation is then automatically downloaded from the UniProt database. The sequence information and identifiers for each labeled protein are parsed from the UniProt file and stored within the database in XLink-DB. If available, the PDB code associated with each protein is also retrieved from the UniProt annotation.

FIG. 21C illustrates an example algorithm for selecting structures related to cross-linked proteins for visualization. For cases where more than one PDB code is associated with one protein, XLink-DB can select and retrieve the PDB structure on the basis of the following rules: First XLink-DB can find all the PDB files that contain structural information covering the cross-linked site. If two cross-linked peptides originate from different protein sequences, which identifies a hetero interaction, all the cocrystal structures containing the two labeled proteins can be put in the candidate pool for later selection. Next, if the cross-linked peptide pair contains identical or overlapping peptide sequences that originate within a single protein sequence, all oligomer structure files containing both sites can be put in the candidate pool. If the cross-linked peptide pair does not fall into either of the two categories above, individual structure files containing both sites can be put into the candidate pool.

FIG. 21C indicates that the algorithm can involve choosing the structure with highest sequence coverage from the candidate pool to use for visualization of the cross-linked peptide pair. The structure with highest sequence coverage can be chosen to allow a best-possible representation of the entire protein and greatest-possible chance to cover cross-linked sites. If no structural file can be found that contains both labeled sites, the algorithm can choose the best individual structures for each labeled site.

Returning to FIG. 21B, after the PDB codes are assigned to each protein, the PDB files for these proteins are automatically downloaded. XLink-DB can computes atom numbers for all cross-linked peptide sites by at least:

The peptide sequence can be mapped to the protein sequence in the PDB file.

The atom numbers and coordinates of every copy of the cross-linked peptide in the PDB file can be identified. The chosen atoms can include the a carbon of the cross-linked lysine residues.

The shortest distance between the two cross-linked sites contained in each cross-linked peptide pair can be calculated from the atomic coordinates of the a carbon atoms.

The associated atom numbers of the cross-linked sites are stored within the database embedded in XLink-DB.

The final data processing procedure shown in FIG. 21B is to compare the uploaded data with an existing protein interaction databases, such as the IntAct and EciD databases. These databases were utilized on the basis of the coverage of protein interaction data; e.g., IntAct is used for human data, EciD is used for E. coli.

In some cases, a node distance can be determined between two cross-linked proteins. The node distance between two cross-linked proteins can serve as a measurement from the reference protein interaction network composed from existing protein interaction database information.

The node distance can provide a numerical value for direct and indirect interactions. For example, if two cross-linked proteins, A and B, are known to interact, the node distance within the reference protein interaction network can be determined to be 0; i.e. a node distance of 0 indicates a direct interaction between the cross-linked proteins A and B.

Otherwise the node distance can be determined to be the smallest number of nodes or proteins that exist in the reference network linking the two cross-linked proteins. For example, suppose the two cross-linked proteins A and B have an interaction involving N=2 interactors (nodes or proteins); e.g., A and B would be linked by additional proteins C and D. The node distance for the interaction can be set to N to indicate an indirect interaction between the cross-linked proteins involving N interactors. In this example, the node distance between A and B linked via interactors C and D would be 2. Many other examples of direct interactions, indirect interactions, and corresponding node distances are possible as well.

If the cross-linked proteins cannot be connected in the reference network, a not-applicable value; e.g., “N/A” can be returned for this computed distance.

Data Visualization

Protein data visualization can be provided using a number of views; e.g., a Network View, a Protein View, a Table View, a Site View, a Search View, and perhaps other views, as shown in FIG. 21A. In Network View, a protein interaction network of the cross-linked peptide data set can be generated with a Cytoscape plugin and be displayed on the left side of the page. A complete set of features available in the Cytoscape plugin are described by Lopez.

Each node in the Network View represents a protein, and each edge represents all the cross-linked peptide pairs linking the two proteins. The users can open files, save files and change the layout and style options using a menu. A toolbox at a right bottom corner of the network graph enables panning and zooming in the graph. Every node and edge in the graph can be selected, dragged and edited.

The page can include three tabs: Visual Style, Filter and Properties. The Visual Style tab allows users to change the color of the nodes, edges and background. The Filter tab allows users to filter the nodes based on the value of attributes. The Properties tab is automatically activated when nodes or edges are selected. When one or more nodes are selected, the interacting partners of the selected nodes can be listed in a table. The name of each interacting partner is converted into a button, which can lead to the Protein View of this protein complex. When one or more edges are selected, the interactions that are represented by the selected edges can be listed in a table. Each interaction is converted to a button, which can lead to the Protein View of the pair.

In addition, the protein interaction network developed with cross-linking data can be compared with previous known protein structural and interaction information. For instance, the size of the node can indicate whether a crystal structure for the protein exists in PDB. The thickness of the edges can be related to the number of cross-linked peptide pairs that have been identified in the data set. For example, thicker lines can be indicative of two or more cross-links. The color of the edge can indicate the distance of connection of the two proteins in reference protein interaction database. As an example, red edges can indicate that direct interactions between linked proteins are found in IntAct or EciD. Also, green edges can indicate that linked proteins have been found to share a common interactor in the reference database and are therefore one node away. As another example, black edges can indicate that linked proteins are more than one node away or were not found in the reference databases. It should be noted that for linkages that contain two peptides from the same protein, the edge color can appear red unless one or more cross-linked pairs are comprised of two peptides with overlapping sequences indicating unambiguous linkage of a homodimer. In these unambiguous homodimer cases, proteins previously known to form homomultimers can appear with red edges, while those not yet known to form homomultimers can appear with green edges. Other visualization schemes, including other coloring schemes, are possible as well.

A Protein View page can contain a Jmol applet on the top if the structure is available, and a result table on the bottom. The user can change basic display options; e.g., using a right-click menu in a Jmol layer.

Part of the page can contain a result table with all the pairs associated with the two proteins. This table can contain data such as peptide sequence, gene name, PDB code, and a number of cross-linked pairs that involve the peptide. The number of cross-linking pairs involving the peptide can measure reactivity and spatial proximity of the labeled site. A larger number of cross-linking pairs can indicate that the labeled site is close to many other sites and thus the labeled site is highly reactive. The users can also use their own favorite structure if they do not appreciate the preassigned structures by inputting the PDB code and the chain IDs for the respective proteins of the own favorite structure.

Buttons on the Protein View page can be used change the display of cross-linked peptide pairs. A “display all” button can illustrate all cross-linked sites associated with the two proteins displayed in the Jmol layer. A “reset complex” button can remove all the cross-linking pairs labeled on the structure. A “display single pair” button can display the selected pair on the structure. A “generate table view” button can change the display to the Table View. Other controls, such as buttons, can be used to change the display as well.

The Table View page can include a result table page. The result table page can contain a top part and a bottom part. The top part can show a title and a link to the network view. The bottom part can show a result table with a peptide sequence, protein accession, PDB code, distance of connection and links to the Protein View. The result table can be sorted by entries within each column by clicking on respective column headings. Each entry in Peptide NB columns can be hyperlinked to the Site View page discussed immediately below. Protein names shown in Protein A/B column within the table can be hyperlinked to relevant UniProt pages for each protein to facilitate further investigation. Similarly, PDB code for peptide NB names can be hyperlinked to the relevant PDB page for additional structure information as needed. A show structure button can produce a protein-level view of the cross-linked pair.

The Site View can show two or more labeled sites in parallel windows to enable visualization of the location of the labeled peptide in the protein. When the crystal structure is available for either protein but not the complex, the site can be highlighted using a predetermined color, such as magenta, on the structure. Otherwise, the entire cross-linked peptide can be highlighted using another predetermined color, such as red, in the protein sequence.

The Search View can be accessed from the home page. The user can search for a protein of interest using a UniProt ID, UniProt accession, or gene name. The user can search for one protein or search for a list of protein IDs. The search can be performed against all the data sets for the selected organism.

Example XLink-DB Results

Two data sets were used to demonstrate the features of XLink-DB. One data set, “Weisbrod et al.”, is a large scale cross-linking experiment performed in our laboratory on intact E. coli cells (see companion manuscript by Weisbrod et al.). The other “Yang et al.” data set was extracted from a recent publication by Yang et al., in which the researchers performed cross-linking on E. coli cell lysate. Both data sets comprise large reported cross-linking data sets and contain several hundred unique cross-linked sites.

There are a few differences in the two experiments. Weisbrod et al. used a customized cross-linker, which is mass spectrometry cleavable and has biotin affinity tag for purification. Yang et al. used commercially available DSS, which is noncleavable. Both data sets used strong cation exchange to enrich high charge peptides. Weisbrod et al. performed avidin capture to enrich biotin-tagged peptides prior to mass spectrometry analysis.

Using XLink-DB to analyze these data sets can provide unique insight into data sets that would have been difficult and time-consuming to get manually. FIG. 22 illustrates a distribution of cross-linked distances extracted from XLink-DB and plotted in Excel. Both data sets show broad distributions of observed cross-linked distances. Disuccinimidyl suberate (DSS) a cross-linker with a relatively short spacer arm length (11.4 A) was applied in the Yang et al. data set. The cross-linker used in the Weisbrod et al. data set has a spacer arm longer than 30 A. However, the fact that both data sets show similar cross-linked distance distributions suggests that cross-linker size is less important than protein flexibility in determination of which protein sites are cross-linked in complex mixtures.

Using XLink-DB, both data sets were compared to the E. coli protein interaction database EciD, while only considering interactions from experimentally derived data. FIG. 23 shows the distribution of the node distances of both data sets and a Monte Carlo simulation of the expected distance for randomly selecting two proteins. Both cross-linking data sets consist of approximately 130 inter-protein interactions. For the Monte Carlo simulation, 130 randomly selected protein pairs were chosen to represent the sample size of the cross-linking experiment. The experiment was repeated 100 times, and the average percentage of each distance is plotted in FIG. 23. On the basis of the Monte Carlo simulation, the most probable expected distance of two randomly chosen proteins is 2 nodes. The majority of the distances for the two cross-linking data sets is below or equal to one node, suggesting that both the Weisbrod et al. and Yang et al. data sets for cross-linking experiments show good correlation with other experimental techniques. Furthermore, the Weisbrod et al. data set contains the highest percentage (25%) of known direct interactors (0 nodes), whereas random simulation predicts about 4%. This suggests that data from either the Weisbrod et al. or Yang et al. cross-linking experiments is significantly different from random data based on existing known interactions from EciD.

Example Computing Network

FIG. 24A is a block diagram of example computing network 2400 in accordance with an example embodiment. In FIG. 24A, servers 2408 and 2410 are configured to communicate, via a network 2406, with client devices 2404 a, 2404 b, and 2404 c. As shown in FIG. 24A, client devices can include a personal computer 2404 a, a laptop computer 2404 b, and a smart-phone 2404 c. More generally, client devices 2404 a-2404 c (or any additional client devices) can be any sort of computing device, such as a workstation, network terminal, desktop computer, laptop computer, wireless communication device (e.g., a cell phone or smart phone), and so on.

The network 2406 can correspond to a local area network, a wide area network, a corporate intranet, the public Internet, combinations thereof, or any other type of network(s) configured to provide communication between networked computing devices. In some embodiments, part or all of the communication between networked computing devices can be secured.

Servers 2408 and 2410 can share content and/or provide content to client devices 2404 a-2404 c. As shown in FIG. 24A, servers 2408 and 2410 are not physically at the same location. Alternatively, servers 2408 and 2410 can be co-located, and/or can be accessible via a network separate from network 2406. Although FIG. 24A shows three client devices and two servers, network 2406 can service more or fewer than three client devices and/or more or fewer than two servers.

Example Computing Device

FIG. 24B is a block diagram of an example computing device 2420 including user interface module 2421, network-communication interface module 2422, one or more processors 2423, and data storage 2424, in accordance with embodiments of the invention.

In particular, computing device 2420 shown in FIG. 24B can be configured to perform one or more functions of the herein-described XLink-DB system, client devices 2404 a-2404 c, network 2406, and/or servers 2408, 2410. Computing device 2420 may include a user interface module 2421, a network-communication interface module 2422, one or more processors 2423, and data storage 2424, all of which may be linked together via a system bus, network, or other connection mechanism 2425.

Computing device 2420 can be a desktop computer, laptop or notebook computer, personal data assistant (PDA), mobile phone, embedded processor, touch-enabled device, or any similar device that is equipped with at least one processing unit capable of executing machine-language instructions that implement and/or perform at least part of the herein-described techniques, algorithms, and methods, including but not limited to the data process algorithm discussed above at least in the context of FIG. 21B, the algorithm for selecting structures discussed above at least in the context of FIG. 21C, one or more functions of the herein-described XLink-DB system, and the method 2500 discussed below in the context of at least FIG. 25.

User interface 2421 can receive input and/or provide output, perhaps to a user. User interface 2421 can be configured to send and/or receive data to and/or from user input from input device(s), such as a keyboard, a keypad, a touch screen, a computer mouse, a track ball, a joystick, and/or other similar devices configured to receive input from a user of the computing device 2420. User interface 2421 can be configured to provide output to output display devices, such as one or more cathode ray tubes (CRTs), liquid crystal displays (LCDs), light emitting diodes (LEDs), displays using digital light processing (DLP) technology, printers, light bulbs, and/or other similar devices capable of displaying graphical, textual, and/or numerical information to a user of computing device 2420. User interface module 2421 can also be configured to generate audible output(s), such as a speaker, speaker jack, audio output port, audio output device, earphones, and/or other similar devices configured to convey sound and/or audible information to a user of computing device 2420.

Network-communication interface module 2422 can be configured to send and receive data over wireless interface 2427 and/or wired interface 2428 via a network, such as network 2406. Wireless interface 2427 if present, can utilize an air interface, such as a Bluetooth®, Wi-Fi®, ZigBee®, and/or WiMAX™ interface to a data network, such as a wide area network (WAN), a local area network (LAN), one or more public data networks (e.g., the Internet), one or more private data networks, or any combination of public and private data networks. Wired interface(s) 2428, if present, can comprise a wire, cable, fiber-optic link and/or similar physical connection(s) to a data network, such as a WAN, LAN, one or more public data networks, one or more private data networks, or any combination of such networks.

In some embodiments, network-communication interface module 2422 can be configured to provide reliable, secured, and/or authenticated communications. For each communication described herein, information for ensuring reliable communications (i.e., guaranteed message delivery) can be provided, perhaps as part of a message header and/or footer (e.g., packet/message sequencing information, encapsulation header(s) and/or footer(s), size/time information, and transmission verification information such as CRC and/or parity check values). Communications can be made secure (e.g., be encoded or encrypted) and/or decrypted/decoded using one or more cryptographic protocols and/or algorithms, such as, but not limited to, DES, AES, RSA, Diffie-Hellman, and/or DSA. Other cryptographic protocols and/or algorithms can be used as well as or in addition to those listed herein to secure (and then decrypt/decode) communications.

Processor(s) 2423 can include one or more central processing units, computer processors, mobile processors, digital signal processors (DSPs), microprocessors, computer chips, and/or other processing units configured to execute machine-language instructions and process data. Processor(s) 2423 can be configured to execute computer-readable program instructions 2426 that are contained in data storage 2424 and/or other instructions as described herein.

Data storage 2424 can include one or more physical and/or non-transitory storage devices, such as read-only memory (ROM), random access memory (RAM), removable-disk-drive memory, hard-disk memory, magnetic-tape memory, flash memory, and/or other storage devices. Data storage 2424 can include one or more physical and/or non-transitory storage devices with at least enough combined storage capacity to contain computer-readable program instructions 2426 and any associated/related data structures.

Computer-readable program instructions 2426 and any data structures contained in data storage 2426 include computer-readable program instructions executable by processor(s) 2423 and any storage required, respectively, to implement and/or perform at least part of the herein-described techniques, algorithms, and methods, including but not limited to the data process algorithm discussed above at least in the context of FIG. 21B, the algorithm for selecting structures discussed above at least in the context of FIG. 21C, one or more functions of the herein-described XLink-DB system, and the method 2500 discussed below in the context of at least FIG. 25.

Example Methods of Operation

FIG. 25 is a flowchart for an example method 2500 for generating a display of multiple protein structures, in accordance with an example embodiment. Method 2500 can be carried out by a computing device, such as computing device 2420 discussed above in the context of at least FIG. 24B.

Method 2500 can begin at block 2510, where a computing device can receive data representing a first protein structure, such as discussed above at least regarding FIG. 21B.

In some embodiments, the computing device comprises a relational database configured to store at least the data representing the interaction between the first protein structure and the second protein structure.

At block 2520, the computing device can receive data representing a second protein structure, such as discussed above at least regarding FIG. 21B.

At block 2530, the computing device can receive data representing an interaction between the first protein structure and the second protein structure, such as discussed above regarding FIGS. 21B and 21C. In some embodiments, the interaction between the first protein structure and the second protein structure can include a cross-link between the first protein structure and the second protein structure, such as discussed above at least regarding FIGS. 21A, 21B, and 21C.

At block 2540, the computing device can generate a display. The display can be configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure, such as shown in at least FIG. 21A.

In some embodiments, generating the display can include: after determining that the co-crystal structure for the first protein structure and the second protein structure is available, generating a first display of the co-crystal structure with an indication of the interaction between the first protein structure and the second protein structure.

In other embodiments, generating the display can include: after determining that the co-crystal structure for the first protein structure and the second protein structure is not available, generating a view of at least one site associated with the interaction between the first protein structure and the second protein structure.

In some embodiments, method 2500 can further include: determining a shortest distance between the first site and the second site, such as discussed above in the context of at least FIGS. 22 and 23.

In other embodiments, method 2500 can further include: determining whether a co-crystal structure for the first protein structure and the second protein structure is available, such as discussed above in the context of at least FIGS. 21B and 21C.

In still other embodiments, method 2500 can further include: performing a comparison of the interaction between the first protein structure and the second protein structure to a plurality of interactions stored in a reference interaction database; and determining a node distance for the interaction based on the comparison. In particular of these embodiments, the comparison can indicate that the interaction between the first protein structure and the second protein structure is a direct interaction. Then, determining the node distance for the interaction based on the comparison comprises determining a node distance of zero for the direct interaction. In other particular of these embodiments, the comparison can indicate that the interaction between the first protein structure and the second protein structure is an interaction involving N interactors, where N>0; i.e., the first protein structure and the second protein structure are indirectly interacting. Then, determining the node distance for the interaction based on the comparison comprises determining a node distance of N for the interaction involving N interactors.

EXAMPLES

The Examples that follow are illustrative of specific embodiments of the invention, and various uses thereof. They are set forth for explanatory purposes only, and are not to be taken as limiting the invention.

Example 1 Liquid Chromatography-Mass Spectrometry (LC-MS) Method

“Real-time Analysis for Cross-linked peptide Technology (ReACT),” combines chemical cross-linking with mass spectrometry (MS) of collisionally induced dissociation (CID) of cleavable cross-linked peptides and permits assignment of cross-linked peptides “on-the-fly.” ReACT enables mass relationship-directed tandem mass spectrometry real-time targeting of released peptides for fragment analysis and identification. This increases the sensitivity, specificity and efficiency of cross-linked peptide identification within a single LC/MS data acquisition. ReACT can also be used to define topological features in protein complexes refractory to conventional structural biology approaches. Thus ReACT is a versatile approach that expedites the characterization of protein-protein interactions and identification of novel binding interfaces.

The general ReACT strategy is outlined in FIG. 1. First, high resolution MS¹ spectra are acquired and deconvoluted to obtain the neutral mass and charge state of all species detected. For any species with charge state equal to or greater than 4+, a high resolution MS² is acquired in a data-dependent fashion (e.g. selection of the top N most abundant 4+ ionic species). Charge state exclusion alternates between two parameter sets depending on the order, n, of each stage of MS^(n) analysis. The set of parameters allows ions with charge state ≧4+ to be selected from high resolution mass spectral acquisition. This is done to focus instrument capabilities on cross-linked species for subsequent tandem mass spectrometry analyses.

Next, the MS² is deconvoluted to obtain the neutral mass and charge state of all species detected. All ions generated during high resolution MS² acquisition for which charge states are assigned are considered during the mass relationship discovery phase of the experiment. By identifying these relationships as the analytes elute from the LC column, ReACT effectively achieves real-time application of analysis strategies for PIR cleavable cross-linkers. More specifically, ReACT analysis identifies spectral features that satisfy a mass relationship that is based on the use of MS-cleavable cross-linkers. Namely, any two released and observed peptide masses added to the reporter mass must equal the observed precursor mass within a user definable mass tolerance, as set forth in equation (1):

PRECURSOR=REPORTER+PEPTIDE₁+PEPTIDE₂,  (1)

where PRECURSOR is the mass of any selected precursor ion, REPORTER is the mass of the reporter ion (after cleavage of the PIR cross-linker) and PEPTIDE_(n) is the mass of the released peptide n. This equation is applied during real-time data acquisition and requires checking N MS² high resolution product ions with each other. This amounts to N²/2 calculations where N is equal to the number of detected isotopic distributions in the MS² pattern.

In some cases, in an effort to make the ReACT method more efficient, masses observed in the MS² spectra are only considered for further analysis if they also satisfy equation (2):

PEPTIDE_(for2)<PRECURSOR−REPORTER−STUMP,  (2)

where STUMP is the residual mass modification which remains on lysine residues after CID cleavage. In other words, a released peptide is considered only if its mass is less than the mass of its precursor ion minus the mass of the reporter ion minus the mass of any residual modifications left on the peptide. This limits the computational space of the calculation by only considering ions lower in mass than PIR partial cleavage products. Partial cleavage products result from incomplete cleavage of the PIR cross-linked products. In such a case, the reporter ion remains covalently linked to one of two peptides involved in the cross-link. While these products can represent a significant contribution to the overall signal of the fragmentation pattern, they are not used in determining whether equation 1 has been satisfied.

In the event that two ion masses from the MS² spectrum satisfy equation 1 and, optionally, equation 2, they are stored for targeted MS³ analysis in the next scan cycle. In this way, no loss of instrument duty cycle occurs during the relationship calculation. During MS³, peptide fragmentation spectra are acquired. Up to two ¹³C offsets are considered to address cases of incorrect monoisotopic peak assignment for cross-linked precursors or product ions. A ¹³C offset is defined as the mass difference in Daltons (Da) between ¹²C and ¹³C.

The final step in the ReACT analysis is to extract the MS3 information and perform a database search with conventional proteome database search tools such as SEQUEST, Mascot, or others. Since ReACT uses mass relationships to direct MS³ events, the number of spectra to be searched scales with the number of relationships found. The selectivity of ReACT results in reduced demand on instrument duty cycle, yet enables specific targeting of cross-linked peptides which are often observed with lower abundance. These species may be missed by traditional data-dependent analyses based on ion abundance alone. The loss of analysis time spent on species that do not meet these criteria is eliminated using ReACT, allowing for the detection of many more cross-linked peptide species than possible with any other current method.

For the ReACT experiments described below, all samples were analyzed on a custom dual linear RF ion trap Fourier transform ion cyclotron resonance mass spectrometer, hereafter referred to as the Velos-FT. The mass spectrometer was directly coupled with a Waters NanoAcquity UPLC system. Cross-linked peptide samples were loaded onto a trap column (3 cm×100 μm i.d.) packed with 200 A Magic-C4AQ (Michrom) using a flow rate of 2 μL/min of 99% solvent A (H₂O containing 0.1% formic acid) and 1% solvent B (acetonitrile containing 0.1% formic acid) where they were washed for a total of 10 minutes. Peptides were then eluted from the trap column and separated by reversed-phase chromatography over an analytical column (30 cm×75 μm i.d.) packed with 100 A Magic-C4AQ at a flow rate of 200 nL/min using a linear gradient from 90% solvent A/10% solvent B to 60% solvent N40% solvent B over 120 min for a 2 hr data acquisition or 240 min for a 4 hr data acquisition. The structure of a ReACT method consists of the following mass spectrometry data acquisition parameters. The first acquisition is a high-resolution precursor acquisition (50,000 resolving power (RP) @ 400 m/z). The second is a high resolution MS² acquisition on ≧4+ charge state isotope distributions. This requires the use of charge state exclusion. Dynamic exclusion is utilized with the following parameters: repeat count=2, repeat duration=15 s, dynamic exclusion list size=500, dynamic exclusion duration=30 s. FT preview mode and predictive automated gain control (pAGC) were not utilized. Monoisotopic precursor selection was used. A series of four RF ion trap MS³ acquisitions were used to acquire fragmentation spectra of peptides observed in cross-linked relationships. These MS³ events include acquisition on the 1+ and 2+ charge states of the peptides found in PIR relationships. Acquiring MS³ spectra on two charge states has been instituted to overcome charge scavenging or unequal distribution of charge upon cleavage of the cross-linked complex.

The ReACT algorithm was written in ion trap control language (ITCL), a native language used with Thermo Electron mass spectrometers.

Example 2 Synthesis of Protein Interaction Reporter (PIR) Cross-Linkers

The PIR cross-linker molecules used in these examples have several engineered features, which aid in the successful identification of cross-linked sites: a biotin affinity tag to allow for enrichment of low abundance cross-linked species, two low energy CID cleavable bonds to release cross-linked peptides and allow for independent sequencing, and a reporter ion to indicate the presence of a cross-linked product.

PIR synthesis was performed using solid phase peptide synthesis (SPPS) methods (Merrifield, 1964, Biochemistry 3:1385-90). The Endeavor 90 (Apptec, Louisville, Ky.) SPPS unit was used for all PIR synthesis steps with the exception of the final N-hydroxy ester (NHX, where X=succinimide or phthalimide) ester formation step. Biotin Rink-PIR (BRink) and Rink-PIR (2Rink) synthesis was as follows. The super acid sensitive resin (SASRIN) with a glycine residue pre-coupled was utilized (Bachem, Munich, Germany). Synthesis of the cross-linker proceeds through fluorenylmethyloxycarbonyl (Fmoc) N-terminally protected SPPS methods (Paramelle et al., 2012, Proteomics 13:438-56). Additions to the resin occur in order and were the following, Fmoc-Lys (biotin), Fmoc-Lys (Fmoc), Fmoc-Rink (all amino acids obtained from Bachem), and succinic anhydride (Sigma-Aldrich, St. Louis, Mo.). 2Rink is synthesized through the same series of steps with the exception of the addition of Fmoc-Lys (biotin). The activated NHS-ester form of the cross-linker is created in a final esterification step immediately prior to use with TFA-NHS. Overall yield for this synthesis was ˜90%. Purity was confirmed by direct infusion ESI-MS analysis. Cross-linker was cleaved from the resin using 1% trifluoroacetic acid (TFA) in methylene chloride and purified using a semi-preparative partisil C18 column (Whatmann, United Kingdom) at low pH to prevent hydrolysis of the NHS ester. BRink and 2Rink were dissolved in dimethylsulfoxide to a concentration of 100 mM.

Biotin Aspartate Proline-PIR (BDP) cross-linker synthesis was also accomplished using Fmoc chemistry as follows. SASRIN-glycine resin was used for the solid support. Amino acid additions to the resin occur in order and were the following: Fmoc-Lys (Biotin), Fmoc-Lys (Fmoc), Fmoc-Pro, Fmoc-Asp (otBu), and succinic anhydride. The activated NHX form of the cross-linker is created in a final esterification step immediately prior to use with TFA-NHX (X=phthalamide or succinimide). Cleavage from the solid support and de-protection of Asp (otBu) was performed simultaneously using 95% TFA/5% methylene chloride. Purification was performed immediately subsequent to Asp de-protection and cleavage via diethyl ether precipitation using 1:15 (cleavage mixture:diethyl ether). Diethyl ether solution was centrifuged at 3400 g to pellet precipitate. Diethyl ether was decanted and pellet was dried to yield ˜90-95% pure BDP-ester. Purity was assayed via direct infusion ESI-MS analysis. BDP was dissolved in dimethylsulfoxide to a concentration of 500 mM to form a stock solution.

Example 3 Data Interpretation and Sequence Identifications

ReACT provides a list of cross-linked relationships observed during an entire data acquisition. Raw mass spectrometry data is converted to mzXML format using ReAdW (ver. 4.3.1). MS² accurate precursor mass and MS³ fragmentation patterns are extracted from the mzXML and converted to Mascot Generic Format (mgf) for Mascot (version 2.3.1) sequence database searches using MzXML2Search (Ver. 4.4) or mzXML was searched directly using SEQUEST (version UWPR2011.01.1). Mascot searches were conducted with a 10 ppm precursor mass tolerance and 0.8 Da fragment ion tolerance. SEQUEST searches were conducted 10 ppm precursor mass tolerance and a 0.36 Da fragment tolerance (0.11 Da fragment offset). The most probable match for each query is accepted (with an expectation value threshold <0.05) and mapped back to the cross-linked relationship for in vitro or standard protein experiments. Sequence databases utilized here include standard proteins (21 sequences including isoforms), SwissProt E. coli (4178 sequences) (http://www.uniprot.org), SwissProt H. sapiens (64,984 sequences) (http://www.uniprot.org), and a database containing cAMP dependent protein kinase regulatory subunit I alpha and beta (RIα and RIβ) and cAMP-dependent protein kinase catalytic domain (pkaC). False discovery during sequence identification for cell experiments was estimated using well-described reverse database search methods. Relationship discovery in real-time required a tolerance of 20 ppm between the putative cross-linked precursor and the cross-linked peptide relationship. This mass tolerance was selected for relationship discovery through balancing sensitivity of relationship discovery with false relationship discovery. False relationship discovery was estimated by performing ReACT analysis on a yeast lysate digest without cross-linker added (<5% of all acquired MS² result in false mass relationships).

Singly charged ions often yield low quality peptide fragmentation patterns when analyzed with ion trap-based instrumentation. The ReACT algorithm includes the ability to target higher charge state released peptides even if the signal-to-noise ratio of higher charge state ions is too low to be selected or even observable within the mass spectrum. It has been shown previously that quadrupole ion storage devices are prone to exclusion of low abundance ions if simultaneously accumulated with more abundant ions (Kim et al., 2005, Science 307(5710):690; Boettcher et al., 2011, Structure 19(2):265). Instrument duty cycle has been reduced as described above. The analysis time liberated by using the real-time targeted approach can be utilized here in the accumulation of low abundance ions. The targeting of low abundance, higher charge ions in some cases results in a cross-linked peptide identification, which would otherwise not be obtainable with 1+ fragmentation patterns alone. This targeting feature of ReACT is illustrated in FIG. 3, where the 2+ ion for the released peptide is observed at a low intensity near the noise level, while the 1+ ion is the base peak in the spectrum. By specifically targeting the 2+ ion for MS³, a fragmentation spectrum useful for peptide sequence identification was acquired. However, MS³ analysis of the 1+ ion of this peptide did not yield sufficient fragment ion information to obtain sequence identification.

Example 4 Structural Modeling

All models were created and rendered using Pymol (Delano Scientific). In vitro PKA structural models were created using coordinates from PDB identifiers 1RGS, 2QCS, and 3IM3. The cAMP binding cassette B in the free RIα was aligned with the corresponding region in the RIα-catalytic subunit complex to show the movement of cAMP binding cassette A. E. coli tryptophanase structural model was created using coordinates from PDB identifier 2OQX. E. coli 30S ribosome structural model was created using coordinates from PDB identifier 3FIH. RNA sequence in the E. coli ribosome was omitted from the rendering process. The human nucleosome structural models were created using coordinates from PDB identifier 3A6N.

Example 5 In Vitro Cross-Linked Protein Analysis

A set of purified proteins were labeled to illustrate that ReACT is useful for real-time analysis of PIR cross-linked peptides.

Alcohol dehydrogenase (S. cerevisiae), α-lactalbumin (Bos taurus), carbonic anhydrase (Bos taurus), cytochrome C (Equus caballus), hemoglobin (Homo sapiens), ribonuclease A (Bos taurus), and myoglobin (Equus caballus) were all obtained from Sigma Aldrich (St. Louis, Mo.) and used as received. Each protein was dissolved at a concentration of 1 mg/mL in phosphate buffered saline (PBS) buffer, pH 7.4. The cross-linking reaction was performed by adding BDP-NHS at a final concentration of 1 mM and incubating the reaction solution at room temperature for 1 hour with constant mixing. A second sample of ribonuclease A was labeled using 2Rink at the same concentration from the multiple cross-linker experiment. After cross-linking disulfide bonds were reduced using 5 mM tris(2-carboxyethyl)phosphine (TCEP) and the resulting free thiols were alkylated using 10 mM iodoacetamide (IAA). Digestion was carried out at using a 1:200 w/w ratio of sequencing grade modified trypsin (Promega, Madison, Wis.) to protein and incubating at 37° C. overnight with constant mixing. The samples were de-salted using C18 Sep-Pak (Waters Corporation, United Kingdom) and dried in a centrifugal concentrator (Genevac, Gardiner, N.Y.). The cross-linked, digested samples were redissolved in solvent A then stored at −80° C. until LC-MS analysis.

The data resultant from this set of experiments (not shown; see Weisbrod et al., 2013, J. Proteome Res. 12:1569-79) show an unambiguous α-β hemoglobin cross-link, as well as unambiguous homodimeric cross-links supporting protein dimerization of ribonuclease A and carbonic anhydrase. The presence of concentrated tryptic peptides from each protein, approximately 100 times more abundant than cross-linked products, provided a more appropriate test for the algorithm. Some examples within the data were identified with a signal-to-noise ratio of ˜2. This illustrates the ability of ReACT to extract useful information, even from low intensity ions.

One important feature of ReACT is that the algorithm is customizable for use with any mass spectrometry cleavable cross-linker including linkers with mono, bi, or higher order CID cleavage sites.

To demonstrate this flexibility, Ribonuclease A (RNase A) was cross-linked with two different PIR molecules, 2Rink and BDP, 14,20 and the ReACT approach was applied. For this sample, the respective reporter masses were entered into ReACT so that ions matching either the mass relationship for 2Rink or for BDP would be identified as cross-linked peptide pairs. In either case, ReACT selected the released peptide ions that fulfilled the relationships in Equation 1 for MS3 analysis. BDP and 2Rink labeled RNase A digests were mixed in equimolar ratios and four fully identified cross-linked products are discussed next. Of the four, two are obtained from BDP, and two are obtained from 2Rink. All four share a single peptide with a unique second peptide. One pair overlaps between the two linkers (ETAAAKFER-NLTKDR; SEQ ID NOS: 13-14). In FIGS. 4A-4C, this cross-linked site has been identified with both linkers within a single ReACT experiment. These two PIR cross-linkers differ in their engineered cleavage site. In BDP, the proline-aspartate amide bond acts as the low energy cleavage site, whereas, in 2Rink it is the tertiary amine within the Rink core structure. The permanent lysine modification or “stump” mass of these linkers differs (99.032 Da for 2Rink or 197.032 Da for BDP). Therefore, peptides identified with this site have b and y fragment ions with different mass shifts due to the modification (FIGS. 4A and 4B). Although this effort is focused on the initial description and application of ReACT, these results demonstrate the capacity of multiple simultaneous cross-linker analyses with ReACT. This feature of ReACT will benefit sample analyses with multiple cross-linker molecules, e.g., with variable structure lengths, reactivity, or physiochemical properties, and may further increase the number of observed cross-linked sites from cells.

Example 6 ReACT Analysis of Protein-Protein Interactions in E. coli

In vivo cross-linking of E. coli was accomplished as follows. E. coli K12 cell suspensions were harvested at O.D. 0.6-0.8. The cells were pelleted and washed 5 times with 1 mL PBS before cross-linking. A 150 μL cell pellet was re-suspended in 150 mL PBS and biotin-aspartate-proline N-hydroxyphlalamide (BDP-NHP) PIR cross-linker was added to the suspension to a final concentration of 10 mM. The reaction was carried out at 4° C. for 1 hr. The cells were lysed by heating to 95° C. in 4% sodium dodecylsulfate (SDS) 1×Tris buffer at pH 8.5. The sample was ultrasonicated to shear DNA. The sample was centrifuged at 16 kg for 10 min to remove insoluble material. It was then added to a 30 kDa molecular weight cut-off (MWCO) filter (Millipore, Billerica, Mass.) and concentrated by centrifugation at 7.5 kg for 30 min. A protein extract yield of 2.0 mg/mL was determined using a Coomassie Plus assay (Pierce, Rockford, Ill.). The sample was reduced, alkylated, and digested as described above. Strong cation exchange (SCX) fractionation of the sample was performed using Macro SCX Spin Columns (Nest Group Inc., Southborough, Mass.) and ammonium acetate in 25% acetonitrile, 75% water for elution. Fractions were collected at 0, 50, 80, 300, 500, and 1000 mM ammonium acetate. Prior to affinity enrichment each fraction was de-salted using C18 Sep-Pak 50 cc (Waters Corporation, United Kingdom). The fractions were biotin affinity enriched for BDP cross-linked peptide products using Ultralink Monomeric Avidin (Pierce, Rockford, Ill.). To each fraction 300 μL of settled avidin resin was added in 500 μL of 100 mM ammonium bicarbonate. Enriched cross-linked peptide samples were stored at −80° C. until LC-MS analysis.

ReACT has been developed to provide selectivity in LC-MS^(n) analyses to focus on only those ions which are likely cross-linked peptides. This selectivity is illustrated in an example ReACT dataset acquired from E. coli cells (FIG. 4).

ReACT selectivity for cross-linked species is achieved first on the MS¹ precursor stage through exclusion of ions with charge less than or equal to 4+, since two peptides covalently linked will possess on average 4+ charge state or greater. Many potential analytes are present within the spectrum in FIG. 5A; however, ReACT application results in selection of only those ions with 4+ charge state or higher. In fact, the analyte of interest, 718.174 m/z, is the 576th most abundant peak within the spectrum and would likely never have been sampled by conventional intensity-driven data dependent analyses. Requirement of the CID cleavable linker mass relationships to be observed with narrow mass tolerance (±20 ppm) imparts additional specificity in the analysis of the selected high charge state ions. In the example shown, the measurement error between the observed precursor and sum of masses of the relationship (Equation (1)) is less than 1.5 ppm (FIG. 5B). Typically, mass measurement error for observed cross-linked relationships is less than or equal to 5.0 ppm which significantly reduces false relationship discovery. Upon successful relationship detection, ReACT directs MS³ events to automatically acquire fragment ion spectra for sequence identification of the released peptides (1+ and 2+ charge states for each). Both peptides identified in this example belong to tryptophanase (TNAA_(—) ECOLI). The cross-linked sites were mapped onto the existing crystal structure for E. coli tryptophanase (PDB: 2OQX), where the lysine residues highlighted with arrows represent the cross-linked sites in this example (other residues shown in space-filling form indicate other cross-linking sites found; FIG. 5E).

Previously, PIR technology was employed without ReACT to study PPIs and topologies in vivo within E. coli (Zheng et al., 2011, Mol. Cell Proteomics 10(10):M110.006841). A total of 65 cross-linked peptide pairs were identified using previously published mass spectrometry analysis methods and informatics tools. Conclusive identification of these 65 cross-linked pairs was a labor intensive process, requiring multiple LC-MS runs, multiple sample preparations, and significant efforts in data processing and analysis.

In contrast, ReACT enabled analysis of 519 fully identified cross-linked peptide pairs in E. coli, where both released peptides were identified using SEQUEST with false discovery rate (FDR) below 5% (data not shown; see Weisbrod et al., 2013, J. Proteome Res. 12:1569-79). Because identification of each peptide proceeds via independent MS³ in ReACT, it is possible that only a single peptide is identified by MS³ while the other peptide fragmentation pattern fails to yield a conclusive assignment at the 5% FDR cutoff. Within E. coli, an additional 539 cross-linked relationships were observed in this category. In these cases, accurate released peptide masses and the number of observed matching fragment ions were used to make putative sequence assignments to the peptides above the 5% FDR threshold. Even though the observed SEQUEST score for these ions did not fall within the 5% FDR cutoff, in all cases the accurate peptide mass and the largest number of matching fragment ions search yielded the top scoring SEQUEST candidate. Inclusion of these assignments increased the total number of cross-linked pairs to 1058 cross-linked peptides from E. coli (data not shown; see Weisbrod et al., 2013, J. Proteome Res. 12:1569-79). ReACT greatly advances the ability to identify cross-linked peptides from intact cellular systems and has enabled acquisition of the first set of cross-linked peptides from eukaryotic cells (FIG. 5).

ReACT is a shotgun proteomics approach that advances peptide sequence identification for peptides in cross-linked relationships. Identified peptides are used to infer protein identity. However, in contrast to typical shotgun proteomics experiments where identification of many peptides from a single protein supports that protein or protein family's presence within the sample, a single cross-linked peptide may be the only reactive site identified from an entire protein sequence. It should be noted that this same issue exists for all large-scale cross-linking and post-translational modification studies. To date, this remains a difficult problem to adequately address in large-scale proteomics data sets where modifications are considered. ReACT analysis results in identification of two peptides cross-linked to each other that may or may not belong to the same protein/family. Within the high confidence E. coli cell data presented here, 81% of the cross-linked sites are reported to have both peptides non-redundant (described by a single protein) within the database. Additionally, 12.4% (88 of 708 identified) one of the peptides associated with a cross-linked site are redundant (peptide sequence shared by multiple proteins). Finally, in only 1.5% (11 of 708 identified) of the cases are both peptides redundant in the database. (Data not shown; see Weisbrod et al., 2013, J. Proteome Res. 12:1569-79.)

For peptides that are redundant among two or more protein sequences, putative protein identities were inferred through a set of logical criteria derived to address this issue and described here. First, a peptide is preferentially assigned to a single protein from the list if that peptide can be mapped to the same protein as the other peptide in the cross-linked site. This logical assumption is derived from the fact that lysine residues nearby any reacted lysine site will predominantly be within the same protein sequence. Thus, if one of the redundant proteins is the same as the protein that yielded the other non-redundant cross-linked peptide, this entity is chosen. If this step cannot be satisfied, the redundant peptide is preferentially assigned to a protein from the pool of proteins resultant from all non-redundant peptides identified within ReACT data sets. This logical assumption arises from the fact that because the protein was identified as cross-linked on other sites, cross-linker accessibility and reactivity with this protein is demonstrated. If one or more proteins in this pool contain the redundant peptide sequence, the proteins are assigned on the basis of their order of appearance within the database. Finally, if neither of the associations above can be made, a putative protein ID is assigned on the basis of the order of appearance within the entire protein database. With acquisition of larger cross-linking data sets where the number of redundant peptides is likely to become larger, advanced protein assignment methodologies will be implemented. These efforts will rank such assignments on the basis of the frequency of representation of the protein family within the database, relative genomic distance between the two cross-linked proteins (e.g., are the genes for the two proteins within the same operon or under control of a single promoter), established protein interaction databases, or based on proteins uniquely identified in other cross-linked sites (or e-values).

The primary utility of cross-linking data from cells includes the identification of PPIs and topologies directly from their native physiological environment. The size of resultant ReACT datasets present a significant wealth of structural information. Key macromolecular interactions in E. coli and human cells include ribosome and histone structures for which structural data are available and ReACT data on these complexes is discussed below. Nonetheless, the entire datasets of cross-linked peptides from E. coli and human cells are presented in Weisbrod et al., 2013, J. Proteome Res. 12:1569-79 and Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67, which are expressly incorporated by reference herein for all purposes.

In E. coli, ribosomes have two subunits and are comprised of RNA and protein molecules with 56 different protein sequences. FIG. 6 illustrates the E. coli ribosome structure (PDB: 3FIH) with 3 of 4 inter-protein cross-linked pairs identified from cells in this study using ReACT. In this figure, all heterocross-linked peptides are presented where linkage between two different ribosomal protein sequences was observed. For clarity, other ribosomal intra-protein cross-linked pairs (111 cross-linked pairs) that were identified are omitted; however, these cross-links still provide unique topological information such as distance constraints between lysine residues. Also omitted are inter-protein cross-linked pairs between ribosomal and non-ribosomal proteins e.g. elongation factor TU. In the ribosome, we were able to assign 3 of 4 heterodimeric cross-links directly to crystallographic data (all cross-link sites are <25 A). One observed cross-linked pair was not mapped since the available ribosomal crystal structure does not contain these proteins (RL7_(—) ECOLI and RL10_(—) ECOLI). However, this cross-link between RL7_RL10 illustrates how ReACT can provide new information about well-studied systems directly from cells. For the first time we are able to validate crystallographic measurements of ribosome against data obtained directly from cells using ReACT. Many (160<5% FDR) other non-ribosomal heterodimeric linkages are present within these data which allows new knowledge to be gained beyond previously characterized PPIs and topologies.

Interprotein cross-links discovered with ReACT provide new information about protein interactions directly from E. coli cells. These data can be broken down into three separate categories: previously observed, likely, and uncharacterized. To do this, the interprotein cross-link results presented in FIG. 5 were compared to available protein interaction data from Ecocyc.org (EciD—protein interaction database). From this comparison, 39% of the PPIs presented here have been observed previously through alternative experimental techniques (yeast two hybrid, colP, etc.). However, even for these known interactions, the data acquired with ReACT provide new topological information on these and help visualize how these proteins interact as they exist inside cells. Moreover, 50% of the PPIs discovered using ReACT were found within one node of a known interacting pair discovered using other experimental techniques. That is, 50% of the PPI discovered in cells with ReACT include proteins that are known to participate in the same complexes, but not previously known to interact directly. For example, protein A interacts with protein B and protein B interacts with protein C, but protein A is not known to interact directly with protein C based on empirical data. Here, these PPI's are classified as secondary interactors and include for example, N-acetylmuramoyl-L-alanine amidase (AmiA) that has been shown to interact directly with proteins in the 30 s (rpsA and rpsO) and the 50 s (rplD) ribosome. Although direct cross-linked sites between AmiA and rplD, rpsA, or rpsO were not observed, AmiA was identified as a cross-linked product with rplB (a known direct interaction partner of rplD) of the 50 s ribosome with two unique sites. Although this and other interactions appear in existing databases as secondary interactions, in vivo cross-linking results made possible with ReACT illustrate they are present in cells close to one another and can be linked directly together. If these proteins are not directly interacting, the cross-linking data suggests they are at least participating in the same complexes at the same time with nonrandom relative orientation. In summary, 89% of the interactions identified with ReACT are previously known as direct or secondary interactors. Excitingly, ReACT yields new topological data on all these interactions as they exist in cells.

Example 7 In Vivo Cross-Linking and PPI Identification in HeLa Cells

HeLa cells were grown at 37° C. under a humidified atmosphere containing 5% CO₂ in Dulbecco's modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin until they reached 80% confluence. Cells were harvested by trypsinization and collected into centrifuge tubes. The cells were pelleted and washed 5 times with 1 mL PBS before cross-linking. A 150 μL cell pellet was re-suspended in 150 mL PBS and BDP-NHP cross-linker was added to the suspension with a final concentration of 10 mM. The reaction was carried out at 4° C. for 1 hr. The cells were lysed by heating to 95° C. in 4% sodium dodecylsulfate (SDS) lx Tris buffer at pH 8.5. The sample was ultrasonicated to shear DNA. The sample was centrifuged at 16 kg for 10 min to remove insoluble material. It was then added to a 30 kDa molecular weight cut-off (MWCO) filter (Millipore, Billerica, Mass.) and concentrated by centrifugation at 7.5 kg for 30 min. A protein extract yield of 2.0 mg/mL was determined using a Coomassie Plus assay (Pierce, Rockford, Ill.). The sample was reduced alkylated and digested as described above for the BSA sample. Strong cation exchange (SCX) fractionation of the sample was performed using Macro SCX Spin Columns (Nest Group Inc., Southborough, Mass.) and ammonium acetate in 25% acetonitrile, 75% water for elution. Fractions were collected at 0, 50, 80, 300, 500, and 1000 mM ammonium acetate concentration. Prior to affinity enrichment each fraction was de-salted using C18 Sep-Pak 50 cc (Waters Corporation, United Kingdom). The fractions were biotin affinity enriched for BDP cross-linked peptide products using Ultralink Monomeric Avidin (Pierce, Rockford, Ill.). To each fraction 300 μL of settled avidin resin was added in 500 μL of 100 mM ammonium bicarbonate. Enriched cross-linked peptide samples were stored at −80° C. until LC-MS analysis.

Although fewer in number (260 cross-links at 5% false discovery rate (FDR)), it is important to note that HeLa cell data were generated from fewer biological replicates than the E. coli data above. Nevertheless, these efforts represent the first report of a large-scale cross-linked peptide dataset from a human cell line. A majority of the identified cross-linked peptide relationships from E. coli and HeLa cells were observed with mass errors <5 ppm, even though the tolerance for cross-linked peptide relationship discovery was set to ±20 ppm (FIGS. 20A-20B; see also Weisbrod et al., 2013, J. Proteome Res. 12:1569-79 and Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67). Additionally, a majority of the cross-linked peptide pairs detected and presented here resulted from cross-link types designated as “intra-protein” (FIGS. 6A, 6D), where both peptides originated within the same protein sequence. Homodimer cross-links and intraprotein cross-links both are likely present in this category, since no comprehensive effort has been made to differentiate the two types.

The distributions of cross-linked peptide types observed were similar between E. coli and HeLa cells. More than 100 inter- and 100 intra-protein cross-linked peptides were identified with ReACT at less than 5% false discovery. However, many so-called “unambiguous homodimeric” cross-linked peptides where two identical sequences that could have only have originated from a cross-linked homodimer were observed. For unique proteins involved in cross-linked peptide relationships, the predicted cellular localization is shown in FIGS. 6B, 6E. Protein interaction networks for both E. coli and HeLa cells were constructed using ReACT data (FIGS. 6C, 6F). Proteins found in many cross-linked relationships are indicated as central nodes in these networks and are labeled with their Uniprot protein identifier. Connections between nodes are thick if the cross-link was identified at <5% FDR or thin if identified with the accurate mass and fragment ion method. Protein nodes are colored according to sub-cellular localization. These are the first interaction networks derived from cross-linked cell data.

Among the discovered inter-protein linkages, many of these proteins are known to co-localize, including 79 cross-linked peptide pairs identified from histone proteins for which co-crystal structure data are available. These histone protein data indicate that PIR molecules cross-link proteins within the cell nucleus. In fact, nuclear proteins represent the largest fraction of cross-linked proteins identified in this study, comprising 29% of the total (FIG. 6E). Many of the inter-protein linkages involve proteins known to co-localize which provides strong evidence that ReACT can yield new information on biologically-relevant interactions.

These investigations applied a two-stage approach. The first stage consists of enrichment and shotgun proteomics identification of PIR labeled proteins. In this stage, 15,415 unique peptides were identified at less than 1% FDR, corresponding to 3348 proteins that are putative reactive targets with the PIR cross-linker (data not shown; see Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67). The second stage consisted of affinity enrichment of PIR labeled peptides allowing for the identification of the cross-linked site of interaction. A unique feature of PIR technology is that identification of each peptide in a cross-linked complex proceeds independently. Peptide mass determination and fragmentation spectral acquisition events and subsequent database searches allow each peptide to be identified independent of the other linked peptide. Furthermore, each identification event is also evaluated against a reverse sequence database so that every peptide sequence can be selected above a chosen FDR threshold. Application of these techniques to human cells resulted in 368 identified cross-linked peptide pairs at 5% FDR. The 5% FDR threshold refers to setting an E-value threshold on the peptide assignments from a SEQUEST search of the MS³ spectra against the UniProt human database containing forward and reverse protein sequences such that 5% of the identified peptides passing the E-value threshold result from a match to a reverse sequence. (A table of these 368 cross-linked peptide pairs including observed peptide masses, peptide sequences, and protein descriptions, as well as annotated fragment ion spectra for each of the peptides in these 368 cross-linked peptide pairs, is shown in Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67.) In addition to the 368 cross-linked peptide pairs for which both peptides were identified at 5% FDR, the data set presented here also included 532 additional cross-linked peptide pairs for which only one peptide was identified at less than 5% FDR but the second peptide was identified greater than 5% FDR. The peptides with less confident identifications (>5% FDR) were assigned to the top scoring peptide sequence identified from a SEQUEST search matching both in accurate precursor mass and greatest number of fragment ions. It is important to note that although high quality fragmentation information was not obtained for one of the released peptides from these cross-linked peptide pairs their masses were still measured with high mass accuracy and contain a BDP modified internal lysine residue. These data (not shown; see Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67) highlight a persistent challenge for all cross-linking studies in that high quality fragment spectra are required for both peptides to yield confident cross-linked peptide pair identification. This is one area in particular where future improvements to mass spectrometry methods and informatics will help overcome the challenges faced with cross-linking experiments. Additionally improvements to cross-linker chemical design that would produce released peptides of primarily charge state 2+ and 3+, along with application of different digestion enzymes could contribute to overcoming challenges in this area. By combining these 532 cross-linked peptide pairs with higher confidence set of 368 cross-linked peptide pairs and filtering for redundancy yields a total of 783 unique cross-linked peptide pairs. The mean mass error for the PIR relationships for these 783 cross-linked peptide pairs was 2.9 ppm with over 84% (664) measured at less than 5 ppm mass error as can be seen in the histogram included in FIG. 8.

The data were further analyzed using a recently developed online software tool and database for cross-linking results named XLink-DB. XLink-DB automates several important analyses for large scale cross-linking data sets including generating an interaction network view, comparing observed interactions to known protein interaction databases, and mapping of cross-links onto known structural data. FIG. 9A illustrates a protein interaction network generated from the 648 unique cross-linked peptide pairs from human cells. The network consists of 307 nodes representing the identified cross-linked proteins connected by 446 edges representing observed intraprotein and interprotein cross-links. Highly connected hub nodes are highlighted with a larger node size and their UniProt identifier. Major hubs include histone proteins, ribosomal proteins, and heterogeneous ribonucleoproteins. Importantly, such a protein interaction network generated using chemical cross-linking contains a depth of information beyond what similar protein interaction networks generated by affinity pull-down methods contain. In addition to the identities of the interacting proteins, topological information about the interacting regions of these proteins is contained in the cross-linked residues. It is worth noting that for cross-linked peptides to be observed by the approach described in this paper must have existed in relatively close proximity and orientation to one another billions to trillions of times (assuming femtomole to picomole sensitivity levels for peptides using modern mass spectrometers) during the reactive lifetime of the cross-linker (λ˜8 min in neutral pH aqueous buffer). Thus what could be viewed as limitations of current cross-linking technology actually provide a valuable benefit in that nonspecific protein-protein interactions, which are a commonly an Achilles' heel for affinity purification-mass spectrometry (AP-MS) approaches, are likely to be less frequently detected because the linkage takes place on proteins within their native environment. Additionally, linkage of only two or a few specific lysine residues in two protein sequences indicates that the two proteins are close to one another in cells with a specific relative orientation so as to allow only specific cross-links to be formed. These two features: 1) high frequency of being close to one another and 2) high frequency of being close to one another with a specific orientation, are hallmarks of specific protein interactions. Therefore, chemical cross-linking technologies can provide this level of detail and will eventually be exploited more effectively to help better understand specific protein interactions in cells.

The protein interaction network was processed with XLink-DB to compare the protein interactions discovered by cross-linking with previously known interactions present in the IntAct database (Kerrien et al., 2012, Nucleic Acids Res. 40:D841-46). A histogram of nodal distances between discovered and known interactions is displayed in FIG. 9B. The majority interprotein cross-links have a distance of either one or two, meaning that the two cross-linked proteins are not known to directly interact in the IntAct database but they either share a common interacting partner, which connects them, or their interacting partners are known to directly interact. Although there are only 34 cross-links that have an IntAct nodal distance of zero, it should be noted that there are several examples of well-known interacting proteins that do not exist as direct interacting partners in the IntAct database. For example the interaction between histones H31 (UniProt accession P68431) and H4 (UniProt accession P62805) are well established interacting partners in the nucleosome complex however have a nodal distance of one according to IntAct. Such cases are inevitable reflections of incomplete knowledge and annotations in protein interaction databases. Despite these instances, protein interactions with nodal distances of 1 or greater potentially represent newly discovered protein interactions. For example, the E3 ubiquitin-protein ligase CBL-B where lysine 468 was cross-linked with lysine 29 of the high mobility group protein B1. These two proteins have a nodal distance of one in IntAct, however are observed as direct interacting partners in this study. As described below, cross-links identify the endoplasmic reticulum membrane protein dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 1 (aka ribophorin-1) and the outer membrane glycoprotein stabilin-1 as direct interacting partners although they are separated by two nodes in IntAct.

Nodes in the network are shaded according to their top subcellular location obtained from the UniProt database. As expected for many of the nodes, interactions are discovered between proteins from the same subcellular compartment. However, there are also interactions between proteins from different subcellular compartments, which are readily explainable. For example interactions between nuclear and cytoplasmic proteins are to be expected, with many reports of proteins moving between these compartments through the nuclear pore 20 (Schwikowski et al., 2000, Nat. Biotechnol. 18:1257-61). It is also worth noting that the majority of proteins have multiple entries in UniProt for subcellular location so although the top entries for two cross-linked proteins may not match, subsequent entries may overlap. For example, the cross-link between alpha actinin 4, which has a top subcellular annotation as nuclear and a secondary annotation of cytoplasmic, and beta actin, which has a top subcellular annotation of cytoplasmic. In addition it is unreasonable to expect that the UniProt annotation for the subcellular localization of proteins is both complete and comprehensive, therefore it is quite possible that two proteins of seemingly different subcellular locations are identified as cross-linked. FIG. 9C illustrates the percentage of proteins from the various subcellular locations in a pie diagram. Importantly all major subcellular locations are represented and the large percentage of cytosolic and nuclear proteins indicates adequate penetration of the PIR cross-linker into cells, a conclusion supported by the fluorescence microscopy data in FIGS. 10A-10C.

By attempting to map the 691 unique cross-linked sites from 783 cross-linked peptides to available x-ray crystal structures in the Protein Data Bank, Euclidean distances between the linked alpha carbon atoms were obtained for 130 cross-links. The measured distances spanned a range from 5.1 to 54.3 Å with a median distance of 14.9 Å as can be seen in a histogram in supplemental Fig. S4. The distances on average are about 20 Å less than the maximum spacer arm length for BDP-PIR (˜35 Å) with ˜95% of the total measured distances less than 35 Å. The seven cases where measured distances exceeded 35 Å can be rationalized by considering factors such as the flexibility of protein structures in solution. For example the largest distance mapped (54.3 Å) corresponds to a cross-link between K37 of H3 and K91 of H4. Being that H3K37 is located on the very flexible N-terminal tail of H3 it is possible the actual distance between the cross-linked sites is shorter than that measured from the crystal structure. It is also possible that this cross-link results from the linkage between H3 and H4 from stacked nucleosome particles, rather than within a single nucleosome complex. As an example of another explainable case; the cross-link between K488 and K797 of DNA topoisomerase 2-alpha was mapped as an intraprotein cross-link with a distance of 42.2 Å, however it is possible this cross-link may span a shorter distance existing between two identical subunits of DNA topoisomerase 2-alpha being that it is known to form a homodimer (33). The PDB structure (1LWZ) used to map the distance of the cross-linked site for this protein only contains a monomeric structure so we were only able to map this distance as an intralink. The observed distances match well with other studies in our laboratory applying PIR cross-linking in E. coli (17-19). These distances also appear consistent with those observed and/or predicted in other studies that employed cross-linkers with much smaller linker arms such as DSS or BS3 (spacer arm length ˜11.4 Å) (5, 11, 16, 34). For example Herzog et al. measured the median Euclidean distances between alpha carbons for 70 interprotein and 287 intraprotein DSS cross-linked peptide pairs from protein phosphatase 2A complexes to be 19.6 Å and 15.4 Å respectively (11). These measurements suggest that factors other than cross-linker length play a role in the determination of which sites are observed from large-scale cross-linking studies. The cross-links, which we were not able to map onto crystal structures, provide valuable new information on interaction topologies for many proteins that have no existing and/or partially resolved crystal structures. As can be seen by the pie chart in FIG. 8C no structural information exists in the Protein Data Bank for most (over 80%) of the total cross-linked sites from both the high and low confidence data sets identified in this study. For example cross-links observed in the highly disordered N-terminal tails of the core histone proteins, which are absent from nucleosome crystal structures. Additionally cross-links membrane proteins prohibitin 1 (PHB) and prohibitin-2 (PHB2) can provide new insights into the topology of interaction for these proteins. These and other examples are discussed in more detail below.

Of the 368 high confidence cross-linked pairs, 284 consisted of two peptides from within the same protein sequence, meaning they are either intraprotein linkages or interprotein linkages from homo-multimers. These two types are not easily distinguished except for cases where the two peptides are exactly the same sequence (peptide homodimer) or share some overlapping sequence, which only occurs once per protein molecule. There are 12 such unambiguous homodimers in the present data set.

The high number of observed intraprotein and homodimer cross-links is to be expected for several reasons. First, intraprotein cross-links are formed in greater abundance because of the fact that once one reactive group of the cross-linker reacts with a protein molecule the second functional group becomes tethered and is constrained to react with a free amine site nearby, often times within the same molecule. Furthermore, self-interacting proteins are anticipated to be a predominant type of specific protein-protein interaction because of colocalization and a relatively high local concentration of binding partners (Ispolatov et al., 2005, Nucleic Acids Res. 33:3629-35; Kuriyan et al., 2007, Nature 450:983-90). Select examples of unambiguous homodimer cross-links are discussed in more detail below.

In addition to enabling identification of traditional cross-linked peptides, the data presented in this Example also demonstrate the ability to identify cross-linked peptides containing additional post-translational modifications including methylation, and dimethylation on lysine and arginine, trimethylation lysine, and acetylation on lysine. It has been previously noted that cross-linked sites observed in E. coli were also sites of lysine acetylation (Bruce, 2012, Proteomics 12:1565-75). This raises interesting questions about the relative reactivity of these particular lysine residues as well as the influence of these and nearby lysine sites in defining protein topology and regulation of protein interactions. It seems plausible that lysine residues, which are targets of post-translational modification, reside on the surface of the protein to increase accessibility. These specific residues also appear to represent local “hot spots” of reactivity for modifying enzymes as well as cross-linker molecules. The application of chemical cross-linking to understand the impact of post-translational modifications on protein topology and interactions is currently uncharted territory, but could greatly accelerate understanding of the relevance of post-translational modifications in biological systems. A primary factor that has inhibited this advance is the large increase in database search space when allowing for the possibility of post-translational modifications that is further exacerbated by the N² increase in search space encountered when attempting to assign two peptide sequences from a single precursor mass (Maiolica et al., 2007, Mol. Cell. Proteomics 6:2200-11). Therefore, confident identification of variable post-translational modifications from complex samples becomes impractical, if not intractable, when working with traditional, non-cleavable cross-linkers. The cleavable feature of PIR cross-linkers allows for individual accurate mass measurements to be made on the released peptides, eliminating the N² increase in search space, and allowing for the confident identification of variable post-translational modifications. The possibility of identifying post-translational modifications in the cross-linked peptide data set from HeLa cells was investigated. Excitingly, confident identification was achieved on 93 unique cross-linked peptide pairs, which contained additional post-translational modifications including mono-, di-, and tri-methylation on Lys as well as acetylation on Lys residues (data not shown; see Chavez et al., 2013, Mol. Cell Proteomics 12(5):1451-67). These 93 cross-linked peptides contain 21 unique sites of modification on 13 different proteins. Importantly, these data are the first reported cross-linked peptides containing in vivo post-translational modifications known to be important for regulating protein topology and interactions and having a direct impact on protein function. To date, identification of modified cross-linked peptides from genome scale databases has not been demonstrated by any other approach.

Eighty-two cross-linked peptide pairs were identified from histones, which also contained additional post-translational modifications. All of the observed histone cross-linked sites and modifications observed are included in Table 1.

TABLE 1 Histone cross-links with modifications. peptide 1 peptide 2 pep1 pep2 peptide 1* peptide 2* Prot. 1 Prot. 2 mod. veri- mod. veri- xlink xlink (SEQ ID NO) (SEQ ID NO) (UniProt) (UniProt) fication‡ fication‡ site{circumflex over ( )} site{circumflex over ( )} K[142.11]STGG TK[325.13]QTA sp P68431 sp P68431 H3K9me, 14 4 K[325.13]APR R (28) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[156.13]STGG TK[325.13]QTA sp P68431 sp P68431 H3K9me2, 14 4 K[325.130APR R (28) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[142.11]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me, 14 18 K[325.13]APR K(19) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[156.13]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me2, 14 18 K[325.13]APR K(19) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[156.13]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me2, H3K23ac, 14 18 K[325.13]APR K[170.110AAR H31_HUMAN H31_HUMAN Uniprot Uniprot (18) (29) +3 +2 K[156.13]SAPA YQK[325.13ST sp P68431 sp P68431 H3K27me2, 36 56 TGGVK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[156.13]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me2, 37 56 TGGVK[156.13] ELLIR (31) H31_HUMAN H31_HUMAN H3K36me2, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, 36 18 TGGVK[325.13] K (19) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[142.11]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me2, H3K23ac, 14 18 K[325.13]APR K[170.11]AAR H31_HUMAN H31_HUMAN Uniprot Uniprot (18) (29) +3 +2 K[156.13]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me2, 37 56 TGGVK[142.11] ELLIR (31) H31_HUMAN H31_HUMAN H3K36me, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me2, 36 56 TGGVK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN H3K36me, K[142.11]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, H3K23ac, 36 18 TGGVK[325.13] K[170.11]AAR H31_HUMAN H31_HUMAN Uniprot Uniprot KPHR (30) (29) +2 +2 K[156.13]STGG YQK[325.13]ST sp P68431 sp P68431 H3K9me2, 14 56 K[325.13]APR ELLIR (31) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[156.13]SAPA TK[325.13]QTA sp P68431 sp P68431 H3K27me2, 36 4 TGGVK[325.13] r (33) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[156.13]STGG RGGVK[325.13] sp P68431 sp P62805 H3K9me2, 14 44 K[325.13]APR R (34) H31_HUMAN H4_HUMAN Uniprot (18) +3 K[156.13]SAPA TK[325.13]QTA sp P68431 sp P68431 H3K27me2, 37 4 TGGVK[156.13] R (33) H31_HUMAN H31_HUMAN H3K36me2, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, 36 18 TGGVK[325.13] K (19) H31_HUMAN H31_HUMAN H3K37me2, K[156.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, H3K23ac, 37 18 TGGVK[142.11] K[170.11]AAR H31_HUMAN H31_HUMAN H3K36me, Uniprot K[325.13]PHR (29) +2 +2 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, H3K23ac, 37 18 TGGVK[156.13] K[170.11]AAR H31_HUMAN H31_HUMAN H3K36me2, Uniprot K[325.13]PHR (29) +2 +2 Uniprot (30) K[156.13]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me2, 36 56 TGGVK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN H3K37me2, K[156.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]TESH sp P68431 sp P04908 H3K27me2, 36 119 TGGVK[325.13] HK (35) H31_HUMAN H2A1B_ Uniprot KPHR (30) +2 HUMAN +1 K[156.13]SAPA K[325.13]TESH sp P68431 sp P04908 H3K27me2, 37 119 TGGVK[156.13] HK (35) H31_HUMAN H2A1B_ H3K36me2, K[325.13]PHR +2 HUMAN +1 Uniprot (30) K[156.13]SAPA K[325.13]TESH sp P68431 sp P04908 H3K27me2, 37 119 TGGVK[142.11] HK (35) H31_HUMAN H2A1B_ H3K36me, K[325.13]PHR +2 HUMAN +1 Uniprot (30) K[156.13]SAPA K[156.13]STGG sp P68431 sp P68431 H3K9me2, 36 14 TGGVK[325.13] K[325.13]APR H31_HUMAN H31_HUMAN Uniprot Uniprot KPHR (30) (18) +2 +3 K[142.11]STGG K[170.14]SAPA sp P68431 sp P68431 H3K9me, H3K27me3, 14 36 K[325.13]APR TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot Uniprot (18) KPHR (30) +3 +2 K[142.11]STGG K[156.13]SAPA sp P68431 sp P68431 H3K9me, H3K27me2, 14 36 K[325.13]APR TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot Uniprot (18) KPHR (30) +3 +2 K[156.13]SAPA K[156.13]STGG sp P68431 sp P68431 H3K27me2, H3K9me2, 37 14 TGGVK[142.11] K[325.13]APR H31_HUMAN H31_HUMAN H3K36me, Uniprot K[325.13]PHR (18) +2 +3 Uniprot (30) K[156.13]SAPA K[156.13]STGG sp P68431 sp P68431 H3K27me2, H3K9me2, 37 14 TGGVK[156.13] K[325.13]APR H31_HUMAN H31_HUMAN H3K36me2, Uniprot K[325.13]PHR (18) +2 +3 Uniprot (30) K[156.13]SAPA K[170.14]STGG sp P68431 sp P68431 H3K27me2, H3K9me3, 37 14 TGGVK[156.13] K[325.13]APR H31_HUMAN H31_HUMAN H3K36me2, Uniprot K[325.13]PHR (18) +2 +3 Uniprot (30) K[156.13]SAPA RGGVK[325.13] sp P68431 sp P62805 H3K27me2, 37 44 TGGVK[156.13] R (34) H31_HUMAN H4_HUMAN H3K36me2, K[325.13]PHR +2 Uniprot (30) K[156.13]SAPA LAHYNK[325.13] sp P68431 sp P33778 H3K27me2, 37 85 TGGVK[156.13] R (36) H31_HUMAN H2B1B_ H3K36me2, K[325.13]PHR +2 HUMAN +2 Uniprot (30) K[156.13]SAPA TK[325.13]QTA sp P68431 sp P68431 H3K27me2, 36 4 TGGVK[325.13] R (19) H31_HUMAN H31_HUMAN H3K37me2, K[156.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, 37 18 TGGVK[156.13] K (19) H31_HUMAN H31_HUMAN H3K36me2, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]STGG sp P68431 sp P68431 H3K27me2, 36 9 TGGVK[325.13] K (37) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[142.11]SAPA K[156.13]STGG sp P68431 sp P68431 H3K27me, 36 14 TGGVK[325.13] K[325.13]APR H31_HUMAN H31_HUMAN Uniprot KPHR (30) (18) +2 +3 K[156.13]SAPA RGGVK[325.13] sp P68431 sp P62805 H3K27me2, 36 44 TGGVK[325.13] R (34) H31_HUMAN H4_HUMAN Uniprot KPHR (30) +2 K[156.13]SAPA RGGVK[325.13] sp P68431 sp P62805 H3K27me2, 37 44 TGGVK[142.11] R (34) H31_HUMAN H4_HUMAN H3K36me, K[325.13]PHR +2 Uniprot (30) K[156.13]SAPA RGGVK[325.13] sp P68431 sp P62805 H3K27me2, 36 44 TGGVK[325.13] R (34) H31_HUMAN H4_HUMAN H3K36me, K[142.11]PHR +2 Uniprot (30) K[156.13]STGG K[156.13]STGG sp P68431 sp P68431 H3K9me2, H3K9me2, 14 14 K[325.23]APR K[325.13]APR H31_HUMAN H31_HUMAN Uniprot Uniprot (18) (18) +3 +3 K[156.13]SAPA TK[325.13]QTA sp P68431 sp P68431 H3K27me2, 37 4 TGGVK[142.11] R (33) H31_HUMAN H31_HUMAN H3K36me, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me2, 37 18 TGGVK[142.11] L (19) H31_HUMAN H31_HUMAN H3K36me, K[325.13]PHR +2 +3 Uniprot (30) K[156.13]SAPS YQK[325.13]ST sp P84243 sp P84243 H3K27me2, 37 56 TGGVK[156.13] ELLIR (31) H33_HUMAN H33_HUMAN H3K36me2, K[325.13]PHR +3 Uniprot (32) K[325.13]STGG TK[325.13]QTA sp P68431 sp P68431 H3K14ac, 9 4 K[170.11]APR R (28) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[325.13]QLAT TK[325.13]QTA sp P68431 sp P68431 H3K14ac, 18 4 K[170.11]AAR R (28) H31_HUMAN H31_HUMAN Uniprot (29) +2 +3 K[170.14]STGG TK[325.13]QTA sp P68431 sp P68431 H3K9me3, 14 4 K[325.13]APR R (28) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[170.14]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me3, 14 18 K[325.13]APR K (19) H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 K[170.14]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me3, 37 56 TGGVKK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN Uniprot PHR (30) +3 +3 GLGK[325.13]G LLLPGELAK sp P62805 sp P62807 H4K16ac, 12 108 GAK[170.11]R [325.13]HAVSE H4_HUMAN H2B1C_ Uniprot (38) GTK (39) HUMAN +3 K[170.14]STGG K[325.13]QLAT sp P68431 sp P68431 H3K9me3, H3K23ac, 14 18 K[325.13]APR K[170.11]AAR H31_HUMAN H31_HUMAN Uniprot Uniprot (18) (29) +3 +2 K[170.11]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27ac, 36 56 TGGVK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[170.14]SAPA YQK[325.13]ST sp P68431 sp P68431 H3K27me3, 36 56 TGGVK[325.13] ELLIR (31) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[170.14]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me3, 36 18 TGGVK[325.13] K (19) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[325.13]QLAT K[325.13]STGG sp P68431 sp P68431 H3K14ac, H3K14ac, 18 9 K[170.11]AAR K[170.11]APR H31_HUMAN H31_HUMAN Uniprot Uniprot (29) +2 +3 K[170.14]SAPA TK[325.13]QTA sp P68431 sp P68431 H3K27me3, 36 4 TGGVK[325.13] R (28) H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +3 K[170.14]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27me3, H3K23ac, 36 18 TGGVK[325.13] K[170.11]AAR H31_HUMAN H31_HUMAN Uniprot Uniprot KPHR (30) (29) +2 +2 K[325.13]QLAT K[325.13]SAPA sp P68431 sp P68431 H3K14ac, H3K36me, 18 27 K[170.11]AAR TGGVK[142.11] H31_HUMAN H31_HUMAN Uniprot Uniprot (29) KPHR (30) +2 +2 K[170.14]SAPA K[325.13]TESH sp P68431 sp P04908 H3K27me3, 36 119 TGGVK[325.13] HK (40) H31_HUMAN H2A1B_ Uniprot KPHR (30) +2 HUMAN +1 K[170.14]SAPA K[170.14]STGG sp P68431 sp P68431 H3K27me3, H3K9me3, 36 14 TGGVK[325.13] K[325.13]APR H31_HUMAN H31_HUMAN Uniprot Uniprot KPHR (30) (18) +2 +3 K[170.11]SAPA K[325.13]QLAT sp P68431 sp P68431 H3K27ac, 37 18 TGGVKK[325.13] K (19) H31_HUMAN H31_HUMAN Uniprot PHR (30) +2 +3 K[325.13]QLAT K[325.13]SAPA sp P68431 sp P68431 H3K14ac, H3K36me2, 18 27 K[170.11]AAR TGGVK[156.13] H31_HUMAN H31_HUMAN Uniprot Uniprot (29) KPHR (30) +2 +2 KQLATK[325.13] K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 23 36 AAR (29) TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KQLATK[325.13] K[142.11]STGG sp P68431 sp P68431 H3K9me, 23 14 AAR (29) K[325.13]APR H31_HUMAN H31_HUMAN Uniprot (18) +2 +3 KQLATK[325.13] K[156.13]STGG sp P68431 sp P68431 H3K9me2, 23 14 AAR (29) K[325.13]APR H31_HUMAN H31_HUMAN Uniprot (18) +2 +3 GGK[325.13]GL K[156.13]STGG sp P62805 sp P68431 H3K9me2, 8 14 GK (41) K[325.13]APR H4_HUMAN H31_HUMAN Uniprot (18) +3 KTESHHK[325.1] K[156.13]STGG sp P04908 sp P68431 H3K9me2, 125 14 AK (42) K[325.13]APR H2A1B_ H31_HUMAN Uniprot (18) HUMAN +3 GK[325.13]GGK K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 5 36 (43) TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KQLATK[325.13] K[142.11]SAPA sp P68431 sp P68431 H3K27me, 23 36 AAR (29) TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KQLATK[325.13] K[325.13]SAPA sp P68431 sp P68431 H3K36me, 23 27 AAR (29) TGGVK[142.11] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KQLATK[325.13] K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 23 37 AAR (29) TGGVK[156.13] H31_HUMAN H31_HUMAN H3K36me2, K[325.13]PHR +2 +2 Uniprot (30) KQLATK[325.13] K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 23 37 AAR (29) TGGVK[142.11] H31_HUMAN H31_HUMAN H3K36me, K[325.13]PHR +2 +2 Uniprot (30) KQLATK[325.13] K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 23 36 AAR (29) TGGVK[325.13] H31_HUMAN H31_HUMAN H3K37me, K[142.11]PHR +2 +2 Uniprot (30) KTESHHK K[156.13]SAPA sp P04908 sp P68431 H3K27me2, 125 36 [325.13]AK TGGVK[325.13] H2A1B_ H31_HUMAN Uniprot (42) KPHR (30) HUMAN +2 KQLATK[325.13] K[156.13]SAPA sp P68431 sp P68431 H3K27me2, 23 36 AAR (29) TGGVK[325.13] H31_HUMAN H31_HUMAN H3K37me2, K[156.13] +2 +2 Uniprot (30) GK[325.13]GGK GLGK[325.13]G sp P68431 sp P62805 H4K16ac, 5 12 (43) GAK[170.11]R H31_HUMAN H4_HUMAN Uniprot (38) +2 KQLATK[325.13] K[170.14]STGG sp P68431 sp P68431 H3K9me3, 23 14 AAR (29) K[325.13]APR H31_HUMAN H31_HUMAN Uniprot (18) +2 +3 KQLATK[325.13] K[325.13]STGG sp P68431 sp P68431 H3K14ac, 23 9 AAR (29) K[170.11]APR H31_HUMAN H31_HUMAN Uniprot (18) +2 +3 K[325.13]QLAT K[325.13]STGG sp P68431 sp P68431 H3K14ac, 18 9 K (19) K[170.11]APR H31_HUMAN H31_HUMAN Uniprot (18) +3 +3 KQLATK[325.13] K[325.13]SAPA sp P68431 sp P68431 H3K36me3, 23 27 AAR (29) TGGCK[170.14] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KQLATL[325.13] K[325.13]SAPS sp P68431 sp P84243 H3K36me3, 23 27 AAR (29) TGGVK[170.14] H31_HUMAN H33_HUMAN Uniprot KPHR (32) +2 KQLATK[325.13] K[170.14]SAPA sp P68431 sp P68431 H3K27me3, 23 36 AAR (29) TGGVK[325.13] H31_HUMAN H31_HUMAN Uniprot KPHR (30) +2 +2 KTESHHK K[170.14]STGG sp P04908 sp P68431 H3K9me3, 125 14 [325.13]AK K[325.13]APR H2A1B_ H31_HUMAN Uniprot (42) HUMAN +3 *identified cross-linked peptide sequence with mass of modifications indicated in brackets following the modified residue. Modifications are: 142.11-mono-methylation, 156.13-di-methylation, 170.11-acetylation, 170.14-tri-methylation, 325.13-BDP stump mass indicating cross-linked residue. ‡Modification checked against data contained in UniProt for known modification sites. {circumflex over ( )}amino acid residue number for cross-linked site starting with initial Met = 1.

These data, discussed in further detail below, provide unique insight into the structure of histone proteins and how their topology changes with various modification states. It is important to note that the lysine side chains linked by our cross-linker must be unmodified because the activated ester reactive groups will not react with acetylated or methylated amines. Furthermore, it is worth noting that six peptides were assigned to have modified Lys or Arg residues as their C-terminal residue. Although there are reports of trypsin cleaving at methylated Lys, there is a possibility these represent incorrect assignments because of the lack of specificity of trypsin to cleave at modified Lys or Arg. However six peptides out of 736 total peptides in the high-confidence set of cross-links corresponds to ˜0.8% of peptide identifications, well below the 5% FDR threshold.

Unambiguous Cross-Linked Homodimers.

If one accepts the theory that protein colocalization lies at the origin of all protein-protein interactions and that most interactions between paralogs evolved from ancestral homodimer interactions, then understanding topologies of interaction between homodimers is at the heart of understanding how and why protein molecules interact with one another. Because of their importance, homo-oligomeric interactions are of intense interest for drug development effort for the treatment of a myriad of human diseases including cancer and HIV. HSP90 is one such homodimer that has significant clinical significance in cancer. One example of an unambiguous homodimer cross-link is the peptide FYEAFSK434NLK spanning residues 428-437 (bold underline indicates cross-linked residue) from heat shock protein 90-beta (HS90B). The mass spectra identifying the HS90B homodimer cross-link are shown in FIGS. 11A-11C. HSP90 proteins are highly conserved, essential molecular chaperones that assist in the proper folding and stabilization of proteins as well as regulation of cellular signaling pathways. The location of the homodimer cross-link was mapped onto the homologous structure for HS90 homodimer from yeast. The identified cross-linked site lies near the transition between the catalytic protein binding domain of HS90 that serves to bind substrates and contains the catalytic loop, and the C-terminal dimerization domain FIG. 11D. Prediction of protein disorder with the VSL2 disorder predictor using the sequence from HS90B indicates that K434 is located near a transition from ordered to disordered structure, which appear to be more susceptible to cross-linker reaction in large scale studies. Five additional cross-links were observed in HS90B including two with K434 (K434-K606, and K346-K434) linking this site with sites in the C-terminal dimerization domain and in the disordered amphiphilic loop implicated in client protein interactions respectively. Of the three additional HS90B cross-links, two are in the N-terminal region (K52-K106, K198-K203) and one is in the C-terminal region K606-K623. Although these additional cross-links do not provide unambiguous information about the multimeric state of HS90B, they are nonetheless structurally informative. Recently HSP90 proteins have become the target of anticancer treatments because of their stabilization of several oncogenic factors promoting tumor growth. Two cytosolic isoforms of HSP90 exist in humans, including HS90B (constitutive expression form) and heat shock protein 90-alpha (HS90A) (inducible expression form). These two isoforms share 85% sequence homology and are thought to be the result of a gene duplication event that occurred 500 million years ago. The two isoforms of HSP90 are thought to exist primarily as homodimers however some evidence for alpha-beta homodimers also exists. Interestingly, a hetero-dimer cross-linked peptide pair was identified that included the same site of HS90B (K434), and the peptide FYEQFSK⁴⁴²NIK (SEQ ID NO: 1) spanning residues 436-445 of HS90A. The respective mass spectra used to identify this hetero-dimer cross-linked peptide pair are illustrated in FIG. 12. Sequence alignment of HS90A and HS90B from human and HS90 from yeast (not shown) reveals that all of the lysine residues cross-linked in HS90B are conserved in HS90A and in yeast HS90 except for K204 in yeast and K347 in HS90A, which are both substituted to arginine. As mentioned above the cross-linked residues identified here (HS90B-K434, and HS90A-K442) lie near the interface of the C-terminal dimerization domain and the middle domain of HSP90, which is important for client protein binding and also contains the catalytic loop. Interestingly, both K434 and K623 of HS90B, and K442 of HS90A have been identified as acetylation sites. Acetylation has been shown to regulate HS90 activity and can inhibit its dynamic association with other chaperones and cochaperones. Several studies have correlated HSP90 activity with histone deacetylase (HDAC) activity, suggesting that combination cancer therapy with HSP90 inhibitors and HDAC inhibitors may have a synergistic effect. Although acetylation of these particular lysine residues has not yet been detected in cross-linked peptide relationships, the fact that these sites of acetylation are known to be important for stabilization of protein interactions demonstrates that in vivo cross-linking methods can, in some cases, be used to identify interactions topologies in these same critical regions. The relationships between sites of post-translational modifications that were identified in cross-linked peptides from other proteins are discussed in more detail below.

Another example of a cross-linked homodimer is the mitochondrial enzyme glutamate dehydrogenase (GDH). GDH exists as a homo-hexamer and catalyzes the conversion of glutamate into α-ketoglutarate and ammonia. PIR data allowed identification of the peptide FGK⁴⁷⁹HGGTIPIVPTAEFQDR (SEQ ID NO: 44) as an unambiguous cross-linked homodimer. In a similar situation to the cases discussed above, the cross-linked lysine residue (K479) is also known to be a site of acetylation. GDH has been identified as an in vivo target of the sirtuin SIRT3, although the functional significance of GDH acetylation remains unclear. The cross-linked site exists near a tri-molecular interface at the tip of the antenna domain FIG. 13. The antenna domain is not found in bacterial, plant or fungal GDH and is thought to play an important role in allosteric regulation of GDH.

Extensive Cross-Linking of Histones.

From the high confidence set of 368 cross-linked pairs, 162 (44%) were intra- or interprotein links between histone proteins. Histones are the chief protein components of chromatin, forming a bead like nucleosome core complex around which DNA is coiled. There are five major classes of histones including the core histones H2A, H2B, H3, and H4, and the linker histones H1/H5. Experiments reported here resulted in identification of cross-links in and between each of these classes of histones. A nucleosome particle is comprised of an octameric complex containing two copies of each of the four core histone proteins around which 147 base pairs of DNA is wrapped. The structure of the core histones is highly conserved consisting of a helix-turn-helix-turn-helix motif from which long tails extend. The histone tails are highly disordered in structure and enriched in Lys and Arg residues making them particularly basic. The tails play a particularly important role in epigenetic regulation of chromatin serving as a scaffold for a host of post-translational modifications including methylation, acetylation, phosphorylation, and others. It has been suggested that combinations of these modifications may alter histone topology and interactions serving to regulate chromatin function in a complex chemical language known as the “histone code.” The alkaline property of histones may in part explain why such a large number of cross-links in and among these proteins is present in these data.

Mapping the observed histone cross-links onto the human chromatin x-ray crystal structure (PDB: 3AFA) (Tachiwana et al., 2010, Proc. Natl. Acad. Sci. U.S.A. 107: 10454-59), enabled reconstruction of the assembly of the octamer complex from information contained in the cross-linked sites at multiple levels (intraprotein, homodimer, and interprotein) (FIG. 13). Importantly the information provided by these cross-links sheds light on the structure and orientation of the nucleosome complexes as present in vivo. FIG. 14A illustrates the cross-linker reactive residues observed for each of the four types of core histone proteins. Disordered N-terminal and C-terminal regions not included in the crystal structure were drawn in manually to illustrate the multiple cross-linked sites observed on the histone tails. Interprotein cross-links including unambiguous homodimer cross-links between H3 and H4, and H2A and H2B are displayed on the tetramer structures in FIG. 14B; however, the N-terminal tails are excluded here for clarity. Finally cross-links between the H3-H4 subunits and the H2A-H2B subunits are displayed with the full chromatin structure in FIG. 14C.

Cross-Links Containing Post-Translational Modifications.

Histone H31 was the most heavily post-translationally modified protein detected in this study. In total, 13 unique post-translational modification sites on histone H31 were identified in cross-linked peptide pairs from human cells. These included the acetylation sites H3K14ac, H3K23ac, and H3K27ac, the mono-methylation sides at H3K9me, H3K27me, H3K36me and H3K37me, di-methylation sites H3K9me2, H3K27me2, H3K36me2, and H3K37me2, and tri-methylation sites H3K9me3, and H3K27me3. We have mapped the modifications observed at each site along with the observed cross-links onto the sequence for histone H3 in FIG. 15. It should be noted that except for the cases of unambiguous homodimer cross-links, these data are not able to conclusively distinguish intramolecular from intermolecular linkages in histone tails. Regardless, these results provide interesting insight into the topology of histone H3 and how it is altered with varying post-translational modification. For instance, cross-links between residues K4-K23, K18-K18, and K18-K23 are only observed with unmodified peptides. In contrast cross-links between residues K4-K36, K4-K37, K14-K14, K14-K23, K14-K36, K14-K37, K14-K56, K23-K36, K23-K37, and K37-K56 of histone H3 are only observed with mono-, di-, or tri-methylation present on a site on one of the cross-linked peptides. Linkages unique to acetylation modifications include K4-K18 and K9-K18. Overlap of the histone H3 intralinks with the presence of post-translational modifications is illustrated by the Venn diagram in FIG. 15. Interestingly, linkages between the end of the N-terminal tail (K4) and the base of the tail (K36 and K37) are only observed when there is a di- or tri-methylation at K27. Similarly cross-links between K14 and K23, K36, K37, and K53 are only observed with mono-, di-, or tri-methylation at H3K9. Various degrees of methylation at H3K9 are known to each have distinct effects over chromatin structure and activation or repression of specific genes. Cross-links were observed between H3K14 and K60 of N-actetyltransferase 10 (NAT10), a protein known to acetylate histones and stimulate telomerase activity, when either H3K9me2 or H3K9me3 were present suggesting these modifications could be important for this interaction. The interconversion between the different states of methylation at H3K9 is regulated by a diverse set of methyltransferases and demethylases. Partial chromatographic resolution of cross-linked peptides between residues 14 and 18 containing various degrees of methylation at H3K9 is shown in FIG. 15. As expected, with increasing degrees of methylation the retention time is lengthened on average. In addition, the integrated chromatographic peak areas of each of the modified forms is different, with di-methylation at H3K9 having the largest area and the unmodified form having the smallest area, though it should be noted peak areas may not be directly comparable across modification states because of differing ionization efficiencies. However the ability to chromatographically separate cross-linked peptides with differing modification states opens the possibility to quantify changes to various forms across different biological states employing stable isotope labeling techniques. The information obtained by such measurements would be distinct from global levels of modification at a specific site because of the topological information contained in the cross-linked peptide pair.

For the case of histone H4, acetylation modification was observed at H4K16ac. The intraprotein cross-link between K5-K12 was observed in the presence and absence of H4K16ac. Similarly a cross-link between H4K12 and H2BK108 was observed in the presence and absence of H4K16ac. Acetylation at H4K16ac has been shown to inhibit formation higher order chromatin structure contributing to de-condensation of chromatin fibers. Furthermore the acetylation state of H4K16 has been shown to regulate interactions between various forms of chromatin and interacting proteins including Sir3, ISWI, and Bdf1. We also identified two post-translationally modified sites of elongation factor 1-alpha (EF1A1) in cross-linked relationships including trimethylation on K35 and dimethylation on K54. Both of these modifications have been previously observed in EF1A1 isolated from rabbit reticulocytes. Although the biological roles of methylation on these two sites of EF1A1 have not be characterized, Lamberti et al. propose that these modifications increase the enzymatic activity of EF1A1 (Lamberti et al., 2004, Amino Acids 26:443-48). EF1A1 is a core component of the protein synthesis machinery promoting the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis however has additional roles in cell signaling and apoptosis pathways.

As demonstrated by these results, it is now possible to directly monitor the topological effects of post-translational modifications at discrete sites in proteins using in vivo cross-linking with mass spectrometry. This opens the door to many future proteomics experiments in which the effects of varying levels and types of post-translational modifications across differing biological states can be directly linked to changes in protein topology and interactions.

New insights into interaction topologies. These cross-linking results provide new insight into protein interactions as they exist in the cell. This can be in the form of novel interacting partners or new topological information on known protein-protein interactions for which no previous structural information exists. One such example is the known interacting partners prohibitin (PHB) and prohibitin-2 (PHB2). Prohibitins are highly conserved, ubiquitous, and pleiotropic proteins implicated in a diversity of biological processes including proliferation, regulation of transcription, apoptosis, and cellular senescence. Evidence from yeast suggests prohibitins primarily localize to the inner mitochondrial membrane where PHB and PHB2 (a.k.a. BAP32 and BAP37) assemble into a ring shaped complex of approximately 1.2-1.4 MDa consisting of approximately 14 PHB-PHB2 dimers. The stabilities of PHB and PHB2 are also linked as they are readily degraded in the absence of their respective partner. In addition to their role in mitochondrial function, evidence also indicates prohibitins localize to the nuclear and the plasma membranes where they function in transcriptional regulation and signal transduction. Prohibitins are also emerging as potential therapeutic targets due to evidence implicating them in human health disorders including HIV, cancer. inflammatory disorders, diabetes, and obesity. Therefore there is much interest in understanding the molecular mechanisms by which prohibitins are able to carry out their diverse functions. Membrane proteins such as the prohibitins are notoriously difficult to study with structural techniques such as NMR and x-ray crystallography and unfortunately, structural details on prohibitins are scarce.

Using PIR cross-linking and ReACT in HeLa cells, a cross-link was identified between K201 of PHB and K215 of PHB2. Importantly these sites exist within predicted coiled-coil domains of PHB and PHB2 thought to be important for interaction between prohibitin subunits. Interestingly, the site of in vivo cross-linking between PHB and PHB2 in human cells reported here is conserved in vitro in purified yeast complexes where K204 was identified as cross-linked to K233 of PHB2. To construct a molecular model for the PHB-PHB2 dimer we first obtained homology models for PHB (residues 59-218, with 99.9% confidence) and PHB2 (residues 73 to 239, with 100% confidence) monomers using the protein structure prediction software Phyre2. Both models were constructed using the crystal structure of a core domain of stomatin from Pyrococcus horikoshii(PDB: 3BK6). The monomers were docked using PatchDock using distance constraints derived from the cross-linked residues identified here. The top scoring PHB-PHB2 dimer and PHB-PHB homodimer models from PatchDock are shown in FIG. 16. Although slight differences exist between the homodimer and heterodimer models, the alpha helical C-terminal domains in both of these models are interacting when cross-linking restraints are applied. For comparison, dimer models for these two complexes were generated without cross-linking distance constraint information and are shown in FIGS. 17A-17D. It can be seen that without applying the information from the cross-linked sites the resulting dimer models are quite different with the C-terminal domains on opposite sides of the complex. Despite the previous lack of evidence for any PHB homo-oligomers, these results also provide the first direct evidence for a prohibitin homodimer with an unambiguous peptide homodimer cross-link observed between K201 of PHB. Taken together, these results suggest these lysine sites to be important for homo- and hetero-interactions in human prohibitin. Knowledge of this interaction topology could be of potential use in future development of therapeutics targeting PHB.

Serving as another example of new protein interaction topology revealed in these data is the cross-link between K591 of stabilin-1 (STAB1) and K563 of ribophorin-1 (RPN1). There are no existing structures for either of these proteins in the PDB. RPN1 is an essential component of the N-oligosaccharyl transferase (OST) complex responsible for the transfer of oligosaccharides from dolichol to N-X-(S/T) motifs on nascent membrane proteins. RPN1 has been shown to transiently associate with a subset of newly synthesized membrane proteins immediately upon leaving the Sec61 translocon. Results from in vitro cross-linking experiments have suggested RPN1 serves to bind and deliver substrate proteins to the catalytic core of the OST. However, there is no existing evidence for interaction between RPN1 and STAB1 and these proteins are separated by two nodes in the IntAct database. STAB1 is a transmembrane receptor glycoprotein protein with ascribed functions in endocytosis, angiogenesis, inflammation, cell adhesion, and cell-cell interactions among others. STAB1 contains 7 fasciclin (FAS), 16 epidermal growth factor (EGF)-like, and 2 laminin-type EGF-like domains as well as a C-type lectin-like hyaluronan-binding Link module. The site of cross-linking (K591 of RPN1, K563 of STAB1) links a predicted cytoplasmic domain on RPN1 (residues 457-606) to the second extracellular FAS domain in STAB1 (residues 505-640). This FAS domain also contains a single N-glycosylation motif (NIS, residues 605-607). These results identify STAB1 as a potential novel substrate of RPN1.

Example 7 Cell Penetration of PIR Crosslinkers

For in vivo cross-linking and study of proteins other than membrane surface proteins, cell penetration of the cross-linker is important. The biotin group on PIR molecules provides a useful handle to perform assays and determine molecular penetration into cells. Using gold-coupled nanoparticle antibodies and electron microscopy, previous Rink-based PIR molecules were shown to penetrate and react with proteins in the cytosol of Gram-negative bacteria. To obtain complimentary verification of the membrane permeability of PIR molecules used with HeLa cells in the present study, we used fluorescent confocal microscopy.

For confocal microscopy samples, HeLa cells were cultured as described above in 35-mm Petri dishes with number 1.5 coverglass bottom (Mat Tek, Ashland, Mass.). When the cells reached 80% confluence they were washed five times with PBS buffer and reacted with 1 mm PIR cross-linker for 1 h. at room temperature. After the cross-linking reaction, cells were again washed 5 times with 2 ml PBS and fixed by addition of 10% formalin for 10 min at room temperature. Following fixation, cells were incubated with 0.1% triton X-100 in 1 ml PBS for 10 min. The cells were then incubated with 1 μg/ml NeutrAvidin OR green 488 (Invitrogen, Grand Island, N.Y.) in 1 ml PBS containing 0.1% triton X-100 for 1 h. in the dark with constant shaking. Cells were then washed three times with 2 ml PBS followed by incubation with 1 μg/ml propidium iodide for 10 min in PBS. Confocal fluorescent imaging was performed in the red and green fluorescent channels using a Nikon A1R confocal microscope using a 60× water immersion objective.

Confocal images of fluorophore-coupled avidin on PIR-reacted HeLa cells illustrated PIR penetration into cytoplasm and nuclear regions and labeled sites on intracellular proteins including nuclear proteins (FIG. 9).

Example 8 In Vitro Crosslinking of Protein Kinase A (PKA) Subunits

The ReACT platform can also identify protein interfaces in systems where a complete structure of the complex is not available. To illustrate this, we investigated intermolecular PPIs in between the subunits of the type 1 cAMP-dependent protein kinase (protein kinase A, PKA) holoenzyme.

Although most of the PKA protein structure has been resolved by X-ray crystallography, regions of the protein interface between the R and C subunits remain refractory to conventional structural biology approaches. In the in active state, PKA holoenzyme is composed of two regulatory subunits and two catalytic subunits (R2C2). The regulatory subunit RIα is a 43 kDa protein which consists of an ordered N-terminal region an ordered C-terminal region, and a disordered flexible linker region between the two ordered regions. This flexible region encompasses an inhibitor site that binds to an active site cleft in the C subunit in the inactive holoenzyme. The RIα N-terminal region has been shown to be critical for docking and dimerization with A-Kinase Anchoring Proteins (AKAPs), whereas, the C-terminal region is responsible for substrate binding. Both, the C-terminal and N-terminal ordered domains have been crystallized; however, the flexible, disordered linker region in RIα has not been successfully probed via crystallography. In our in vitro experiment, samples containing RIα alone and RIα together with the catalytic subunit (C) were each cross-linked using the BDP PIR compound.

The catalytic subunit of PKA was expressed from pET15b as an N-terminal 6×His-tag fusion protein in BL21(DE3)pLysS cells (Invitrogen). Expression was induced with 1 mM IPTG when cells reached an OD600≈0.6. Cells were grown at 37° C. for 4 hours and then pelleted by centrifugation at 5000×g for 10 minutes. Cells were lysed by resuspension in 50 mL nickel lysis buffer (20 mM NaPhosphate pH 7.5, 0.5 M NaCl, 20 mM imidazole, 5 mM TCEP, 1 mM benzamidine, one EDTA-free protease inhibitor tablet (Roche), 0.1 μg/mL lysozyme, 2.5 U/mL benzonase (EMD) and 2 mM MgCl₂). Triton X-100 was added to 0.5% and lysates were incubated for 30 minutes at 4° C., followed by centrifugation at 40,000×g for 30 minutes. Cleared lysates were incubated with 2 mL Ni Sepharose 6 FF (GE Healthcare) for 1 h prior to washing in 20 mM NaPhosphate pH 7.5, 0.5 M NaCl, 20 mM imidazole, 5 mM TCEP and elution in 20 mM NaPhosphate pH 7.5, 0.5 M NaCl, 300 mM imidazole, 1 mM dithiothreitol (DTT). Eluate was further polished by gel filtation using a HiLoad 16/600 Superdex 200 column (GE Healthcare) with 25 mM Tris pH 7.5, 200 mM NaCl, 1 mM DTT, 1 mM EDTA as the column buffer. Peak fractions were collected, dialyzed overnight against GF buffer containing 20% glycerol and flash frozen in liquid N₂.

The RIα subunit of human PKA in pGEX6P1 was expressed as a GST-fusion protein in E. coli as above. Cells were lysed in 50 mM Tris HCl, pH 7.5, 500 mM NaCl, 1 mM DTT, 1 mM EDTA, 2 mM MgCl₂, 1 mM benzamidine, one EDTAfree protease inhibitor tablet (Roche), 0.1 μg/mL lysozyme and 2.5 U/ml benzonase (EMD). Triton X-100 was added to 0.5% and lysates were incubated for 30 minutes at 4° C. The protein was purified from cleared lysates using glutathione Sepharose-4B (Amersham Biosciences) followed by extensive washing in lysis buffer. Bound protein was cleaved from the beads overnight with PreScission protease (Amersham Biosciences) and finally purified by size-exclusion chromatography as above. Peak fractions were collected, dialyzed overnight against 20 mM HEPES, 150 mM NaCl, 1 mM EDTA and 1 mM DTT, and flash frozen in liquid N₂.

RIα was cross-linked at a concentration of 1.2 mg/mL with 1 mM BDP-NHS reagent to generate the RI only sample. RIα and pkaC (the PKA catalytic subunit) were incubated in a 1:2 molar ratio with a final concentration of 1.2 mg/mL for 2 hrs at room temperature prior to cross-linking. BDP-NHS cross-linking reagent was added to the R:C sample to 1 mM final concentration.

Cross-linking reactions were allowed to proceed for 1 hr at room temperature and then quenched with 100 mM ammonium bicarbonate. 50 uL aliquots from each sample were set aside for SDS-PAGE analysis (FIG. 19), while the remainder was trypsinized in the solution phase. After cross-linking, disulfide bonds were reduced using 5 mM Tris(2-carboxyethyl)phosphine (TCEP) and the resulting free thiols were alkylated using 10 mM iodoacetamide (IAA). Digestion was carried out at using a 1:200 w/w ratio of sequencing grade modified trypsin (Promega, Madison, Wis.) to protein and incubating at 37° C. overnight with constant mixing. The samples were desalted using C18 Sep-Pak (Waters Corporation, United Kingdom) and dried in a centrifugal concentrator (Genevac, Gardiner, N.Y.). Unreacted and dead-end cross-links were removed using Macro SCX Spin Columns (Nest Group Inc., Southborough, Mass.). The fractions were biotin affinity enriched for BDP cross-linked peptide products using Ultralink Monomeric Avidin (Pierce, Rockford, Ill.). Samples were centrifugally concentrated and re-solubilized using Solvent A in preparation for LC-MS analysis.

ReACT analysis of RIα-only samples enabled identification of three unambiguous RIα homodimer cross-linked peptides indicating proximal sites within the RIα dimer in solution, two of which appeared within the disordered linker region. From the RIα, C mixed samples, one heterodimeric linkage between R:C protomers was identified. In addition, homodimer RIα cross-linked peptides identified within the disordered linker region in RIα-only samples, K59-K59 and K92-K92 were still observed from cross-linking experiments that contained the catalytic subunit. However, the homodimeric cross-linked peptide pair K214-K216 identified in RIα-only samples was not observed from these mixed samples. The loss of K214-K216 cross-linked peptides and the appearance of inter-protein cross-linked pairs between RIα and C demonstrate topological features of the RIα dimer are altered upon binding the catalytic domain, consistent with the recognized importance of allostery in this complex.

To better illustrate cross-linked sites on PKA identified with ReACT, the observed cross-linked sites were mapped on the measured structures (PDB: 2QCS, 1RGS, 31M3) and flexible linker region as shown in FIG. 18. PKA undergoes a conformational change in which the two cAMP binding cassettes are brought together by a rearrangement of a central alpha helix. Our cross-linking data indicate that this change in conformation allows formation of an additional homodimeric cross-link between K216 and K214. Since it is unknown how the tetrameric PKA holoenzyme is arranged, there are multiple structural models that can explain our cross-linking data. One such model (FIG. 18A) arranges the heterodimer such that the catalytic subunits are placed between the RIα subunits, and upon release of the C subunit, cAMP binding cassette swings towards the dimeric interface (FIG. 18B), allowing the observation of the additional cross-link (K214-K216). Other structural models based on low-resolution SAXS data, and observations from crystal packing of the partial complex place the catalytic subunit on the outside of the tetrameric complex. However, our cross-linking data identifies a new homodimeric interface upon release of the catalytic subunit that is best explained by the model in FIG. 18B.

Example 9 Potential Drug Targets Elucidated Using ReACT

Many of the protein-protein interactions elucidated by the methods disclosed herein are potential drug targets. Three such potential drug targets are described below.

Potential Drug Targets for Cancer.

Heat shock protein 90 (HSP90) is a molecular chaperone that is commonly observed being overexpressed in cancerous cells where it functions to stabilize hundreds of client proteins many of which are known oncoproteins required for cancer cell survival. It therefore is recognized as a potential therapeutic target and many HSP90 inhibitors have been developed and are currently undergoing clinical trials. The disclosed methods were used to identify cross-linked peptides identifying homo-dimer interactions for both the alpha and beta isoforms of HSP90 as well as heterodimer interactions between the alpha (HS90A) and beta (HS90B) isoforms. These are shown in Table 2. Furthermore cross-linked peptide pairs identify interactions between HSP90 and it known co-chaperone Stress-induced-phosphoprotein 1 (STIP1). Drugs that inhibit interactions with HSP90 are thus potentially useful as cancer therapeutics.

TABLE 2 Selected cross-linked peptides identifying HSP90 interactions. Protein1 Protein2 Peptide1 Peptide2 (GenBank No.; (GenBank No.; (SEQ ID NO) (SEQ ID NO) SEQ ID NO) SEQ ID NO) FYEQFSK ⁴⁴³NIK (1)  FYEQFSK ⁴⁴³NIK (1) HS90A HS90A (CAI64495.1; 20) (CAI64495.1; 20) FYEAFSK ⁴³⁵NLK (2) FYEAFSK ⁴³⁵NLK (2) HS90B HS90B (AAH68474.1; 21) (AAH68474.1; 21) FYEQFSK ⁴⁴³NIK (1)  FYEAFSK ⁴³⁵NLK (2) HS90A HS90B (CAI64495.1; 20) (AAH68474.1; 21) FYEQFSK ⁴⁴³NIK (1)  K ⁶²⁴HLEINPDHPIVETLR (3) HS90A HS90B (CAI64495.1; 20) (AAH68474.1; 21) APFDLFENK ³⁴⁷K (4)  FYEQFSK ⁴⁴³NIK (1) HS90B HS90A (AAH68474.1; 21) (CAI64495.1; 20) FYEQFSK ⁴⁴³NIK (1)  K ⁴³⁴AAALEAMK (5) HS90A STIP1 (CAI64495.1; 20) (AAH39299.1; 22) FYEAFSK ⁴³⁵NLK (2) K ⁴³⁴AAALEAMK (5) HS90B STIP1 (AAH68474.1; 21) (AAH39299.1; 22) Cross-linked Lys residues indicated in bold with amino acid residue number in superscript

Potential Drug Targets for Antibiotic Resistance in A. baumannii.

The protein Oxa-23 exhibits carbapenemase activity and is the key resistance function found in the clinically most problematic carbapenem resistant A. baumannii strains. CarO is a carbapenem-associated resistance outer membrane porin, not previously known to interact directly with Oxa-23. CarO is thought to be required for L-ornithine uptake since CarO deficient strains were specifically impaired for growth on L-ornithine. However, resistance to both imipenem and meropenem in multidrug-resistant clinical strains of A. baumannii has been found to be associated with the loss of CarO. These observations suggest that CarO serves a beneficial role in amino acid and possibly other nutrient uptake but this porin is also associated with carbapenem entry into the cell. These findings suggest that one strategy employed by bacteria like A baumannii to increase antibiotic resistance yet maintain active porin function may be to evolve porin interactions with β-lactamase enzymes. Beneficial maximum β-lactam hydrolysis could be achieved by localizing the β-lactamase in the cell where β-lactam concentration is maximal. This is likely to be the point of entry into the cell and, therefore, it may be anticipated that Oxa-23 and CarO form a close interactions. The PIR data acquired using the methods disclosed herein are the first to demonstrate this interaction and provide topological data on this complex. These results, some of which are shown in Table 3, together with the known crystal structures of Oxa-23 and CarO demonstrate that, in cells, Oxa-23 is cross-linked on a periplasmic loop of the CarO structure.

TABLE 3 Selected cross-linked peptides  identifying Oxa-23 and CarO interactions Protein1 Protein2 Peptide1 Peptide2 (GenBank No.; (GenBank No.; (SEQ ID NO) (SEQ ID NO) SEQ ID NO) SEQ ID NO) K ⁶⁰INLYGN  NDIAPYLGFG Oxa-23 CarO ALSR (6) FAPK ¹⁷⁸INK (7) (ACJ39972.1; 23) (ACN32317.1; 24) Cross-linked Lys residues indicated in bold with amino acid residue number in superscript

Potential Drug Targets for A. baumannii Infection of Human Bronchial Cells.

Host cell adhesion constitutes a primary virulence factor. Most bacteria exist in their natural environment attached to surfaces and the majority of bacterial pathogens exploit specific adhesion to host cells as primary virulence factors. In most infectious diseases, adherence of pathogenic organisms to the host through host receptors is the initial event that serves to target the pathogen to a particular location to capture underlying signaling pathways and host cell functions to establish persistent infections. In the gut, lung, skin and other organs, the human epithelial barrier serves as an infectious foothold for many bacterial pathogens and as an entry port for pathogens to disseminate into deeper tissues. Several host and pathogen proteins are known to be required for host cell attachment, such as type 1 pili, P-pili, type IV pili, curli and non-pilus proteins or OmpA. However, how exactly type IV pili mediate attachment remains unknown.

Mutant bacteria that lack one or more of the determinants above often fail to infect cells, as highlighted below. In A. baumannii, three outer membrane proteins (Omps) have been identified as fibronectin-binding proteins: OmpA, TonB-dependent copper receptor, and 34 kDa Omp. It has also been shown that either fibronectin inhibition and neutralization by specific antibodies or AbOmpA neutralization by specific antibodies significantly decreased adhesion of A. baumannii to human lung epithelial cells. Importantly, their data also support the notion that if known, protein-protein interaction binding interfacial regions between A. baumannii outer membrane proteins and host epithelial cellular proteins would be useful targets for disruption and enable novel infection control strategies of MDR A. baumannii.

PIR and ReACT experiments with A. baumannii cells that were incubated with human bronchial epithelial cells resulted in identification of more than 1766 non-redundant cross-linked peptide pairs from 661 proteins. Selected date is shown in Table 4. These include three non-redundant linkages between the known A. baumannii virulence factor, OmpA, and the human protein desmoplakin, which is an obligate component of functional desmosomes that serve as intercellular junctions to tightly link adjacent cells. The desmoplakin site K2714 that observed to be cross-linked to OmpA is within plakin repeat 3 in the subdomain C that binds intermediate filament proteins such as vimentin and epithelial keratins. Thus, interaction of A. baumannii OmpA with desmoplakin could serve to promote pathogen infiltration by disrupting interactions between host cells and providing an anchoring site for pathogen cells. Furthermore, the A. baumannii protein AB57_(—)2521 that was identified linked to OmpA was also observed cross-linked at this site K2714 on desmoplakin, illustrating that OmpA and its binding partner AB57_(—)2521 interact with human desmoplakin within the same region. These data indicate this interaction occurs when OmpA is present in native complexes which are important for host-pathogen interactions. This knowledge of protein interactions as well as regions within proteins that are involved in interspecies binding could lead to novel therapies that disrupt this interaction, prevent or impede bacterial invasion in human lung epithelial cells, decreasing the ability of A. baumannii to infect humans.

TABLE 4 Selected cross-linked peptides identifying  OmpA-desmoplakin interactions. Protein1 Protein2 Peptide1 Peptide2 (GenBank No.; (GenBank No.; (SEQ ID NO) (SEQ ID NO) SEQ ID NO) SEQ ID NO) VFFDTNK ²³⁵SNIK MSAAEAVK ²⁷¹⁴ OmpA Desmoplakin DQYKPEIAK (8) EK (9) (AAR83911.1; 25) (AAA85135.1; 26) TK ³¹⁹EGR (10) MSAAEAVK ²⁷¹⁴ OmpA Desmoplakin EK (9) (AAR83911.1; 25) (AAA85135.1; 26) LSTQGFAWDQPIA MSAAEAVK ²⁷¹⁴ OmpA Desmoplakin DNK ³¹⁷TK (11) EK (9) (AAR83911.1; 25) (AAA85135.1; 26) Cross-linked Lys residues indicated in bold with amino acid residue number in superscript

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Having described the invention in detail and by reference to specific embodiments thereof, it will be apparent that modifications and variations are possible without departing from the scope of the invention defined in the appended claims. More specifically, although some aspects of the present invention are identified herein as particularly advantageous, it is contemplated that the present invention is not necessarily limited to these particular aspects of the invention. 

What is claimed is:
 1. A method for identifying one or a plurality of interacting peptides within a biological system, comprising: (a) obtaining a population of cross-linked precursor peptides produced by digestion of a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker; (b) subjecting the population of cross-linked precursor peptides to mass spectrometry (MS) to produce precursor ions; (c) subjecting precursor ions with a charge state equal to or greater than a cutoff charge state to conditions under which the cleavable PIR cross-linker is cleaved, thereby producing a population of released peptides and cleaved reporter ions; and (d) analyzing the population of released peptides to identify interacting peptides, wherein identifying interacting peptides comprises identifying released peptides that, when added to the mass of the reporter ion, have a combined mass equal to the mass of the corresponding precursor ion.
 2. The method of claim 1, wherein the population of cross-linked precursor peptides are obtained by contacting a biological system with a cleavable protein interaction reporter (PIR) cross-linker to produce cross-linked proteins, and obtaining the cross-linked precursor peptides therefrom.
 3. The method of claim 2, further comprising purifying and digesting the cross-linked proteins to obtain the cross-linked precursor peptides.
 4. The method of claim 2, wherein the biological system comprises a cell, tissue, cell lysate, blood, serum, sputum, or urine.
 5. The method of claim 1, wherein the conditions under which the cleavable PIR cross-linker is cleaved comprise collision-induced dissociation (CID).
 6. The method of claim 1, wherein the population of released peptides in step (d) is analyzed using tandem mass spectrometry (MS²).
 7. The method of claim 1, wherein identifying interacting peptides in step (d) further comprises first identifying released peptides with masses lower than partial cleavage products prior to identifying released peptides that, when added to the mass of the reporter ion, have a combined mass equal to the mass of the corresponding precursor ion.
 8. The method of claim 7, wherein identifying released peptides with masses lower than partial cleavage products comprises identifying released peptides with masses that are less than the mass of the corresponding precursor ion minus the mass of the reporter ion minus the mass of lysine stumps, wherein lysine stumps are residual modifications that remain on lysine residues after cleavage.
 9. The method of claim 1, further comprising determining the identities of the interacting peptides by subjecting the interacting peptides to conditions that cause peptide fragmentation to yield spectra that can be identified from genomic, proteomic, or other large protein sequence databases.
 10. The method of claim 9, wherein the identities of the interacting peptides are determined by triple mass spectrometry (MS³).
 11. The method of claim 1, wherein the cutoff charge state is at least +3
 12. The method of claim 1, wherein the cutoff charge state is at least +4.
 13. The method of claim 1, wherein the cleavable PIR cross-linker comprises formula (I):

(SEQ ID NO: 27) wherein X is H, succinimid-N-yl, or phthalimid-N-yl; and Y is H or a capture moiety.
 14. The method of claim 13, wherein the capture moiety is biotin, a hemagglutinin (HA) tag, or a polyhistidine tag.
 15. The method of claim 13, wherein the cleavage condition is collision-induced dissociation (CID).
 16. A method of identifying a candidate compound for treating cancer comprising: (a) contacting a peptide pair from the group consisting of: (i) (SEQ ID NO: 1) FYEQFSKNIK, (SEQ ID NO: 1) FYEQFSKNIK; (ii) (SEQ ID NO: 2) FYEAFSKNLK,  (SEQ ID NO: 2) FYEAFSKNLK; (iii) (SEQ ID NO: 1 FYEQFSKNIK),  (SEQ ID NO: 2) FYEAFSKNLK; (iv) (SEQ ID NO: 1) FYEQFSKNIK,  (SEQ ID NO: 3) KHLEINPDHPIVETLR; (v) (SEQ ID NO: 4) APFDLFENKK,  (SEQ ID NO: 1) FYEQFSKNIK; (vi) (SEQ ID NO: 1) FYEQFSKNIK,  (SEQ ID NO: 5) KAAALEAMK; and (vii)  (SEQ ID NO: 2) FYEAFSKNLK,  (SEQ ID NO: 5) KAAALEAMK;

with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating cancer.
 17. A method of identifying a candidate compound for treating an antibiotic-resistant infection comprising: (a) contacting a peptide pair comprising KINLYGNALSR (SEQ ID NO: 6) and NDIAPYLGFGFAPKINK (SEQ ID NO: 7) with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating an antibiotic-resistant infection.
 18. A method of identifying a candidate compound for treating A. baumannii infection comprising: (a) contacting a peptide pair from the group consisting of: (i) (SEQ ID NO: 8) VFFDTNKSNIKDQYKPEIAK,  (SEQ ID NO: 9) MSAAEAVKEK; (ii) (SEQ ID NO: 10) TKEGR,  (SEQ ID NO: 9) MSAAEAVKEK; and (iii)  (SEQ ID NO: 11) LSTQGFAWDQPIADNKTK,  (SEQ ID NO: 9) MSAAEAVKEK;

with a plurality of test compounds under conditions suitable for binding of one member of the peptide pair to the other member of the peptide pair; and (b) identifying a test compound that reduces binding of one member of the peptide pair to the other member of the peptide pair relative to a control, wherein the identified test compound is a candidate compound for treating A. baumannii infection.
 19. A cleavable protein interaction reporter (PIR) cross-linker comprising formula (I):

(SEQ ID NO: 27) wherein X is H, succinimid-N-yl, or phthalimid-N-yl; and Y is H or a capture moiety.
 20. The cleavable PIR cross-linker of claim 19, wherein the amino acids are L-amino acids.
 21. A method, comprising: receiving data representing a first protein structure at a computing device; receiving data representing a second protein structure at the computing device; receiving data representing an interaction between the first protein structure and the second protein structure at the computing device; and generating a display using the computing device, wherein the display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.
 22. The method of claim 21, wherein the interaction between the first protein structure and the second protein structure comprises a cross-link between the first protein structure and the second protein structure.
 23. The method of claim 22, wherein the display is configured to show at least a portion of the cross-link between a first site on the first protein structure and a second site on the second protein structure.
 24. The method of claim 23, wherein the method further comprises: determining a shortest distance between the first site and the second site.
 25. The method of claim 21, wherein the computing device comprises a relational database configured to store at least the data representing the interaction between the first protein structure and the second protein structure.
 26. The method of claim 21, further comprising: determining whether a co-crystal structure for the first protein structure and the second protein structure is available.
 27. The method of claim 26, wherein generating the display comprises: after determining that the co-crystal structure for the first protein structure and the second protein structure is available, generating a first display of the co-crystal structure with an indication of the interaction between the first protein structure and the second protein structure.
 28. The method of claim 26, wherein generating the display comprises: after determining that the co-crystal structure for the first protein structure and the second protein structure is not available, generating a view of at least one site associated with the interaction between the first protein structure and the second protein structure.
 29. The method of claim 21, further comprising: performing a comparison of the interaction between the first protein structure and the second protein structure to a plurality of interactions stored in a reference interaction database; and determining a node distance for the interaction based on the comparison.
 30. The method of claim 29, wherein the comparison indicates the interaction between the first protein structure and the second protein structure is a direct interaction, and wherein determining the node distance for the interaction based on the comparison comprises determining a node distance of zero for the direct interaction.
 31. The method of claim 29, wherein the comparison indicates the interaction between the first protein structure and the second protein structure is an interaction involving N interactors, N>0, and wherein determining the node distance for the interaction based on the comparison comprises determining a node distance of N for the interaction involving N interactors.
 32. A computing device, comprising: a processor; a tangible computer-readable medium configured to comprise instructions that, when executed by the processor, are configured to cause the computing device to perform the method of claim
 21. 33. The computing device of claim 32, wherein the tangible computer-readable medium comprises a non-transitory computer-readable medium.
 34. A tangible computer-readable medium configured to comprise instructions that, when executed by a processor of a computing device, are configured to cause the computing device to perform the method of claim
 21. 35. The tangible computer-readable medium of claim 34, wherein the tangible computer-readable medium is a non-transitory computer-readable medium.
 36. A device, comprising: means for processing; means for receiving data representing a first protein structure; means for receiving data representing a second protein structure; means for receiving data representing an interaction between the first protein structure and the second protein structure; and means for generating a display using the processing means, wherein the display is configured to show at least a portion of: the first protein structure, the second protein structure, and the interaction between the first protein structure and the second protein structure.
 37. The device of claim 36, further comprising: means for displaying at least the display. 